HEADER LYASE 12-MAR-03 1HL2 TITLE CRYSTAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE FROM E. COLI MUTANT TITLE 2 L142R IN COMPLEX WITH B-HYDROXYPYRUVATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLNEURAMINATE LYASE SUBUNIT; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: N-ACETYLNEURAMINIC ACID ALDOLASE, N-ACETYLNEURAMINATE COMPND 5 PYRUVATE LYASE, NALASE; COMPND 6 EC: 4.1.3.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: AT997; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PKK223-3 KEYWDS N-ACETYLNEURAMINATE LYASE, CLASS I ALDOLASE, LYASE, CARBOHYDRATE KEYWDS 2 METABOLISM, SCHIFF BASE EXPDTA X-RAY DIFFRACTION AUTHOR A.C.JOERGER,A.R.FERSHT REVDAT 4 13-DEC-23 1HL2 1 REMARK LINK REVDAT 3 24-FEB-09 1HL2 1 VERSN REVDAT 2 16-MAY-03 1HL2 1 JRNL REVDAT 1 09-MAY-03 1HL2 0 JRNL AUTH A.C.JOERGER,S.MAYER,A.R.FERSHT JRNL TITL MIMICKING NATURAL EVOLUTION IN VITRO: AN N-ACETYLNEURAMINATE JRNL TITL 2 LYASE MUTANT WITH AN INCREASED DIHYDRODIPICOLINATE SYNTHASE JRNL TITL 3 ACTIVITY JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 5694 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12711733 JRNL DOI 10.1073/PNAS.0531477100 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.C.LAWRENCE,J.A.BARBOSA,B.J.SMITH,N.E.HALL,P.A.PILLING, REMARK 1 AUTH 2 H.C.OOI,S.M.MARCUCCIO REMARK 1 TITL STRUCTURE AND MECHANISM OF A SUB-FAMILY OF ENZYMES RELATED REMARK 1 TITL 2 TO N-ACETYLNEURAMINATE LYASE REMARK 1 REF J.MOL.BIOL. V. 266 381 1997 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 9047371 REMARK 1 DOI 10.1006/JMBI.1996.0769 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.IZARD,M.C.LAWRENCE,R.MALBY,G.G.LILLEY,P.M.COLMAN REMARK 1 TITL THE THREE-DIMENSIONAL STRUCTURE OF N-ACETYLNEURAMINATE LYASE REMARK 1 TITL 2 FROM ESCHERICHIA COLI REMARK 1 REF STRUCTURE V. 2 361 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 8081752 REMARK 1 DOI 10.1016/S0969-2126(00)00038-1 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 117329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1164 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9113 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 832 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HL2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1290011750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 117329 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FDY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.60 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 47.99500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CATALYSES THE CONVERION OF N-ACETYLNEURAMINATE TO REMARK 400 N-ACETYL-D-MANNOSAMINE AND PYRUVATE. REMARK 400 REMARK 400 ENGINEERED MUTATION LEU 141 ARG, CHAINS A, B, C AND D REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 297 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG B 296 CA C O CB CG CD NE REMARK 470 ARG B 296 CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG C 142 NE CZ NH1 NH2 REMARK 480 LYS C 222 CD CE NZ REMARK 480 GLU C 279 CG CD OE1 OE2 REMARK 480 LYS D 146 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 271 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLY B 250 N - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 GLY D 250 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 ARG D 253 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG D 253 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 109 -168.68 -116.85 REMARK 500 TYR A 110 -62.81 69.36 REMARK 500 ASP A 130 66.41 34.55 REMARK 500 MET A 213 39.86 -151.73 REMARK 500 PRO A 268 30.87 -77.09 REMARK 500 PHE B 109 -169.46 -115.65 REMARK 500 TYR B 110 -64.45 71.17 REMARK 500 MET B 213 39.74 -152.56 REMARK 500 PRO B 268 29.18 -79.99 REMARK 500 TYR C 110 -61.09 69.04 REMARK 500 ASP C 130 59.43 35.13 REMARK 500 MET C 213 40.34 -156.99 REMARK 500 PRO C 268 34.47 -75.95 REMARK 500 TYR D 110 -65.09 73.65 REMARK 500 MET D 213 41.31 -154.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PY A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PY B 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PY C 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PY D 808 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FDY RELATED DB: PDB REMARK 900 N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH HYDROXYPYRUVATE REMARK 900 RELATED ID: 1FDZ RELATED DB: PDB REMARK 900 N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REMARK 900 REDUCTION REMARK 900 RELATED ID: 1NAL RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: N-ACETYLNEURAMINATE LYASE ; CHAIN: 1, 2, 3, 4; REMARK 900 EC: 4.1.3.3 DBREF 1HL2 A 1 1 PDB 1HL2 1HL2 1 1 DBREF 1HL2 A 2 297 UNP P06995 NPL_ECOLI 1 296 DBREF 1HL2 B 1 1 PDB 1HL2 1HL2 1 1 DBREF 1HL2 B 2 297 UNP P06995 NPL_ECOLI 1 296 DBREF 1HL2 C 1 1 PDB 1HL2 1HL2 1 1 DBREF 1HL2 C 2 297 UNP P06995 NPL_ECOLI 1 296 DBREF 1HL2 D 1 1 PDB 1HL2 1HL2 1 1 DBREF 1HL2 D 2 297 UNP P06995 NPL_ECOLI 1 296 SEQADV 1HL2 ARG A 142 UNP P06995 LEU 141 ENGINEERED MUTATION SEQADV 1HL2 ARG B 142 UNP P06995 LEU 141 ENGINEERED MUTATION SEQADV 1HL2 ARG C 142 UNP P06995 LEU 141 ENGINEERED MUTATION SEQADV 1HL2 ARG D 142 UNP P06995 LEU 141 ENGINEERED MUTATION SEQRES 1 A 297 MET ALA THR ASN LEU ARG GLY VAL MET ALA ALA LEU LEU SEQRES 2 A 297 THR PRO PHE ASP GLN GLN GLN ALA LEU ASP LYS ALA SER SEQRES 3 A 297 LEU ARG ARG LEU VAL GLN PHE ASN ILE GLN GLN GLY ILE SEQRES 4 A 297 ASP GLY LEU TYR VAL GLY GLY SER THR GLY GLU ALA PHE SEQRES 5 A 297 VAL GLN SER LEU SER GLU ARG GLU GLN VAL LEU GLU ILE SEQRES 6 A 297 VAL ALA GLU GLU ALA LYS GLY LYS ILE LYS LEU ILE ALA SEQRES 7 A 297 HIS VAL GLY CYS VAL SER THR ALA GLU SER GLN GLN LEU SEQRES 8 A 297 ALA ALA SER ALA LYS ARG TYR GLY PHE ASP ALA VAL SER SEQRES 9 A 297 ALA VAL THR PRO PHE TYR TYR PRO PHE SER PHE GLU GLU SEQRES 10 A 297 HIS CYS ASP HIS TYR ARG ALA ILE ILE ASP SER ALA ASP SEQRES 11 A 297 GLY LEU PRO MET VAL VAL TYR ASN ILE PRO ALA ARG SER SEQRES 12 A 297 GLY VAL LYS LEU THR LEU ASP GLN ILE ASN THR LEU VAL SEQRES 13 A 297 THR LEU PRO GLY VAL GLY ALA LEU LYS GLN THR SER GLY SEQRES 14 A 297 ASP LEU TYR GLN MET GLU GLN ILE ARG ARG GLU HIS PRO SEQRES 15 A 297 ASP LEU VAL LEU TYR ASN GLY TYR ASP GLU ILE PHE ALA SEQRES 16 A 297 SER GLY LEU LEU ALA GLY ALA ASP GLY GLY ILE GLY SER SEQRES 17 A 297 THR TYR ASN ILE MET GLY TRP ARG TYR GLN GLY ILE VAL SEQRES 18 A 297 LYS ALA LEU LYS GLU GLY ASP ILE GLN THR ALA GLN LYS SEQRES 19 A 297 LEU GLN THR GLU CYS ASN LYS VAL ILE ASP LEU LEU ILE SEQRES 20 A 297 LYS THR GLY VAL PHE ARG GLY LEU LYS THR VAL LEU HIS SEQRES 21 A 297 TYR MET ASP VAL VAL SER VAL PRO LEU CYS ARG LYS PRO SEQRES 22 A 297 PHE GLY PRO VAL ASP GLU LYS TYR LEU PRO GLU LEU LYS SEQRES 23 A 297 ALA LEU ALA GLN GLN LEU MET GLN GLU ARG GLY SEQRES 1 B 297 MET ALA THR ASN LEU ARG GLY VAL MET ALA ALA LEU LEU SEQRES 2 B 297 THR PRO PHE ASP GLN GLN GLN ALA LEU ASP LYS ALA SER SEQRES 3 B 297 LEU ARG ARG LEU VAL GLN PHE ASN ILE GLN GLN GLY ILE SEQRES 4 B 297 ASP GLY LEU TYR VAL GLY GLY SER THR GLY GLU ALA PHE SEQRES 5 B 297 VAL GLN SER LEU SER GLU ARG GLU GLN VAL LEU GLU ILE SEQRES 6 B 297 VAL ALA GLU GLU ALA LYS GLY LYS ILE LYS LEU ILE ALA SEQRES 7 B 297 HIS VAL GLY CYS VAL SER THR ALA GLU SER GLN GLN LEU SEQRES 8 B 297 ALA ALA SER ALA LYS ARG TYR GLY PHE ASP ALA VAL SER SEQRES 9 B 297 ALA VAL THR PRO PHE TYR TYR PRO PHE SER PHE GLU GLU SEQRES 10 B 297 HIS CYS ASP HIS TYR ARG ALA ILE ILE ASP SER ALA ASP SEQRES 11 B 297 GLY LEU PRO MET VAL VAL TYR ASN ILE PRO ALA ARG SER SEQRES 12 B 297 GLY VAL LYS LEU THR LEU ASP GLN ILE ASN THR LEU VAL SEQRES 13 B 297 THR LEU PRO GLY VAL GLY ALA LEU LYS GLN THR SER GLY SEQRES 14 B 297 ASP LEU TYR GLN MET GLU GLN ILE ARG ARG GLU HIS PRO SEQRES 15 B 297 ASP LEU VAL LEU TYR ASN GLY TYR ASP GLU ILE PHE ALA SEQRES 16 B 297 SER GLY LEU LEU ALA GLY ALA ASP GLY GLY ILE GLY SER SEQRES 17 B 297 THR TYR ASN ILE MET GLY TRP ARG TYR GLN GLY ILE VAL SEQRES 18 B 297 LYS ALA LEU LYS GLU GLY ASP ILE GLN THR ALA GLN LYS SEQRES 19 B 297 LEU GLN THR GLU CYS ASN LYS VAL ILE ASP LEU LEU ILE SEQRES 20 B 297 LYS THR GLY VAL PHE ARG GLY LEU LYS THR VAL LEU HIS SEQRES 21 B 297 TYR MET ASP VAL VAL SER VAL PRO LEU CYS ARG LYS PRO SEQRES 22 B 297 PHE GLY PRO VAL ASP GLU LYS TYR LEU PRO GLU LEU LYS SEQRES 23 B 297 ALA LEU ALA GLN GLN LEU MET GLN GLU ARG GLY SEQRES 1 C 297 MET ALA THR ASN LEU ARG GLY VAL MET ALA ALA LEU LEU SEQRES 2 C 297 THR PRO PHE ASP GLN GLN GLN ALA LEU ASP LYS ALA SER SEQRES 3 C 297 LEU ARG ARG LEU VAL GLN PHE ASN ILE GLN GLN GLY ILE SEQRES 4 C 297 ASP GLY LEU TYR VAL GLY GLY SER THR GLY GLU ALA PHE SEQRES 5 C 297 VAL GLN SER LEU SER GLU ARG GLU GLN VAL LEU GLU ILE SEQRES 6 C 297 VAL ALA GLU GLU ALA LYS GLY LYS ILE LYS LEU ILE ALA SEQRES 7 C 297 HIS VAL GLY CYS VAL SER THR ALA GLU SER GLN GLN LEU SEQRES 8 C 297 ALA ALA SER ALA LYS ARG TYR GLY PHE ASP ALA VAL SER SEQRES 9 C 297 ALA VAL THR PRO PHE TYR TYR PRO PHE SER PHE GLU GLU SEQRES 10 C 297 HIS CYS ASP HIS TYR ARG ALA ILE ILE ASP SER ALA ASP SEQRES 11 C 297 GLY LEU PRO MET VAL VAL TYR ASN ILE PRO ALA ARG SER SEQRES 12 C 297 GLY VAL LYS LEU THR LEU ASP GLN ILE ASN THR LEU VAL SEQRES 13 C 297 THR LEU PRO GLY VAL GLY ALA LEU LYS GLN THR SER GLY SEQRES 14 C 297 ASP LEU TYR GLN MET GLU GLN ILE ARG ARG GLU HIS PRO SEQRES 15 C 297 ASP LEU VAL LEU TYR ASN GLY TYR ASP GLU ILE PHE ALA SEQRES 16 C 297 SER GLY LEU LEU ALA GLY ALA ASP GLY GLY ILE GLY SER SEQRES 17 C 297 THR TYR ASN ILE MET GLY TRP ARG TYR GLN GLY ILE VAL SEQRES 18 C 297 LYS ALA LEU LYS GLU GLY ASP ILE GLN THR ALA GLN LYS SEQRES 19 C 297 LEU GLN THR GLU CYS ASN LYS VAL ILE ASP LEU LEU ILE SEQRES 20 C 297 LYS THR GLY VAL PHE ARG GLY LEU LYS THR VAL LEU HIS SEQRES 21 C 297 TYR MET ASP VAL VAL SER VAL PRO LEU CYS ARG LYS PRO SEQRES 22 C 297 PHE GLY PRO VAL ASP GLU LYS TYR LEU PRO GLU LEU LYS SEQRES 23 C 297 ALA LEU ALA GLN GLN LEU MET GLN GLU ARG GLY SEQRES 1 D 297 MET ALA THR ASN LEU ARG GLY VAL MET ALA ALA LEU LEU SEQRES 2 D 297 THR PRO PHE ASP GLN GLN GLN ALA LEU ASP LYS ALA SER SEQRES 3 D 297 LEU ARG ARG LEU VAL GLN PHE ASN ILE GLN GLN GLY ILE SEQRES 4 D 297 ASP GLY LEU TYR VAL GLY GLY SER THR GLY GLU ALA PHE SEQRES 5 D 297 VAL GLN SER LEU SER GLU ARG GLU GLN VAL LEU GLU ILE SEQRES 6 D 297 VAL ALA GLU GLU ALA LYS GLY LYS ILE LYS LEU ILE ALA SEQRES 7 D 297 HIS VAL GLY CYS VAL SER THR ALA GLU SER GLN GLN LEU SEQRES 8 D 297 ALA ALA SER ALA LYS ARG TYR GLY PHE ASP ALA VAL SER SEQRES 9 D 297 ALA VAL THR PRO PHE TYR TYR PRO PHE SER PHE GLU GLU SEQRES 10 D 297 HIS CYS ASP HIS TYR ARG ALA ILE ILE ASP SER ALA ASP SEQRES 11 D 297 GLY LEU PRO MET VAL VAL TYR ASN ILE PRO ALA ARG SER SEQRES 12 D 297 GLY VAL LYS LEU THR LEU ASP GLN ILE ASN THR LEU VAL SEQRES 13 D 297 THR LEU PRO GLY VAL GLY ALA LEU LYS GLN THR SER GLY SEQRES 14 D 297 ASP LEU TYR GLN MET GLU GLN ILE ARG ARG GLU HIS PRO SEQRES 15 D 297 ASP LEU VAL LEU TYR ASN GLY TYR ASP GLU ILE PHE ALA SEQRES 16 D 297 SER GLY LEU LEU ALA GLY ALA ASP GLY GLY ILE GLY SER SEQRES 17 D 297 THR TYR ASN ILE MET GLY TRP ARG TYR GLN GLY ILE VAL SEQRES 18 D 297 LYS ALA LEU LYS GLU GLY ASP ILE GLN THR ALA GLN LYS SEQRES 19 D 297 LEU GLN THR GLU CYS ASN LYS VAL ILE ASP LEU LEU ILE SEQRES 20 D 297 LYS THR GLY VAL PHE ARG GLY LEU LYS THR VAL LEU HIS SEQRES 21 D 297 TYR MET ASP VAL VAL SER VAL PRO LEU CYS ARG LYS PRO SEQRES 22 D 297 PHE GLY PRO VAL ASP GLU LYS TYR LEU PRO GLU LEU LYS SEQRES 23 D 297 ALA LEU ALA GLN GLN LEU MET GLN GLU ARG GLY HET 3PY A 802 6 HET 3PY B 804 6 HET 3PY C 806 6 HET 3PY D 808 6 HETNAM 3PY 3-HYDROXYPYRUVIC ACID FORMUL 5 3PY 4(C3 H4 O4) FORMUL 9 HOH *832(H2 O) HELIX 1 1 ASP A 23 GLN A 37 1 15 HELIX 2 2 GLY A 46 GLU A 50 5 5 HELIX 3 3 GLU A 50 GLN A 54 5 5 HELIX 4 4 SER A 55 LYS A 71 1 17 HELIX 5 5 SER A 84 GLY A 99 1 16 HELIX 6 6 SER A 114 ASP A 130 1 17 HELIX 7 7 ILE A 139 GLY A 144 1 6 HELIX 8 8 THR A 148 THR A 157 1 10 HELIX 9 9 ASP A 170 HIS A 181 1 12 HELIX 10 10 TYR A 190 GLU A 192 5 3 HELIX 11 11 ILE A 193 GLY A 201 1 9 HELIX 12 12 THR A 209 GLU A 226 1 18 HELIX 13 13 ASP A 228 GLY A 250 1 23 HELIX 14 14 GLY A 250 MET A 262 1 13 HELIX 15 15 ASP A 278 LYS A 280 5 3 HELIX 16 16 TYR A 281 GLU A 295 1 15 HELIX 17 17 ASP B 23 GLN B 37 1 15 HELIX 18 18 GLY B 46 GLU B 50 5 5 HELIX 19 19 GLU B 50 GLN B 54 5 5 HELIX 20 20 SER B 55 LYS B 71 1 17 HELIX 21 21 SER B 84 GLY B 99 1 16 HELIX 22 22 SER B 114 ALA B 129 1 16 HELIX 23 23 ILE B 139 GLY B 144 1 6 HELIX 24 24 THR B 148 VAL B 156 1 9 HELIX 25 25 ASP B 170 HIS B 181 1 12 HELIX 26 26 TYR B 190 GLU B 192 5 3 HELIX 27 27 ILE B 193 GLY B 201 1 9 HELIX 28 28 THR B 209 GLY B 227 1 19 HELIX 29 29 ASP B 228 GLY B 250 1 23 HELIX 30 30 GLY B 250 MET B 262 1 13 HELIX 31 31 ASP B 278 LYS B 280 5 3 HELIX 32 32 TYR B 281 GLN B 294 1 14 HELIX 33 33 ASP C 23 GLN C 37 1 15 HELIX 34 34 GLU C 50 GLN C 54 5 5 HELIX 35 35 SER C 55 LYS C 71 1 17 HELIX 36 36 SER C 84 GLY C 99 1 16 HELIX 37 37 SER C 114 ALA C 129 1 16 HELIX 38 38 ILE C 139 GLY C 144 1 6 HELIX 39 39 THR C 148 THR C 157 1 10 HELIX 40 40 ASP C 170 HIS C 181 1 12 HELIX 41 41 TYR C 190 GLU C 192 5 3 HELIX 42 42 ILE C 193 GLY C 201 1 9 HELIX 43 43 THR C 209 GLU C 226 1 18 HELIX 44 44 ASP C 228 GLY C 250 1 23 HELIX 45 45 GLY C 250 MET C 262 1 13 HELIX 46 46 ASP C 278 LYS C 280 5 3 HELIX 47 47 TYR C 281 GLU C 295 1 15 HELIX 48 48 ASP D 23 GLN D 37 1 15 HELIX 49 49 GLU D 50 GLN D 54 5 5 HELIX 50 50 SER D 55 LYS D 71 1 17 HELIX 51 51 SER D 84 GLY D 99 1 16 HELIX 52 52 SER D 114 ASP D 130 1 17 HELIX 53 53 ILE D 139 GLY D 144 1 6 HELIX 54 54 THR D 148 THR D 157 1 10 HELIX 55 55 ASP D 170 HIS D 181 1 12 HELIX 56 56 TYR D 190 GLU D 192 5 3 HELIX 57 57 ILE D 193 GLY D 201 1 9 HELIX 58 58 THR D 209 GLU D 226 1 18 HELIX 59 59 ASP D 228 GLY D 250 1 23 HELIX 60 60 GLY D 250 MET D 262 1 13 HELIX 61 61 ASP D 278 LYS D 280 5 3 HELIX 62 62 TYR D 281 GLU D 295 1 15 SHEET 1 AA10 VAL A 8 ALA A 11 0 SHEET 2 AA10 GLY A 204 GLY A 207 1 O GLY A 205 N MET A 9 SHEET 3 AA10 VAL A 185 ASN A 188 1 O ASN A 188 N ILE A 206 SHEET 4 AA10 VAL A 161 GLN A 166 1 O GLY A 162 N VAL A 185 SHEET 5 AA10 MET A 134 ASN A 138 1 O MET A 134 N GLY A 162 SHEET 6 AA10 ALA A 102 VAL A 106 1 O VAL A 103 N VAL A 135 SHEET 7 AA10 LYS A 75 HIS A 79 1 O ALA A 78 N SER A 104 SHEET 8 AA10 GLY A 41 VAL A 44 1 O LEU A 42 N ILE A 77 SHEET 9 AA10 VAL A 8 ALA A 11 1 O ALA A 10 N TYR A 43 SHEET 10 AA10 VAL A 8 ALA A 11 0 SHEET 1 BA10 VAL B 8 ALA B 11 0 SHEET 2 BA10 GLY B 204 GLY B 207 1 O GLY B 205 N MET B 9 SHEET 3 BA10 VAL B 185 ASN B 188 1 O ASN B 188 N ILE B 206 SHEET 4 BA10 VAL B 161 GLN B 166 1 O GLY B 162 N VAL B 185 SHEET 5 BA10 MET B 134 ASN B 138 1 O MET B 134 N GLY B 162 SHEET 6 BA10 ALA B 102 VAL B 106 1 O VAL B 103 N VAL B 135 SHEET 7 BA10 LYS B 75 HIS B 79 1 O ALA B 78 N SER B 104 SHEET 8 BA10 GLY B 41 VAL B 44 1 O LEU B 42 N ILE B 77 SHEET 9 BA10 VAL B 8 ALA B 11 1 O ALA B 10 N TYR B 43 SHEET 10 BA10 VAL B 8 ALA B 11 0 SHEET 1 CA22 VAL C 8 ALA C 11 0 SHEET 2 CA22 GLY C 204 GLY C 207 1 O GLY C 205 N MET C 9 SHEET 3 CA22 VAL C 185 ASN C 188 1 O ASN C 188 N ILE C 206 SHEET 4 CA22 VAL C 161 GLN C 166 1 O GLY C 162 N VAL C 185 SHEET 5 CA22 MET C 134 ASN C 138 1 O MET C 134 N GLY C 162 SHEET 6 CA22 ALA C 102 VAL C 106 1 O VAL C 103 N VAL C 135 SHEET 7 CA22 LYS C 75 HIS C 79 1 O ALA C 78 N SER C 104 SHEET 8 CA22 GLY C 41 VAL C 44 1 O LEU C 42 N ILE C 77 SHEET 9 CA22 GLY C 41 VAL C 44 0 SHEET 10 CA22 VAL C 8 ALA C 11 1 O ALA C 10 N TYR C 43 SHEET 11 CA22 LYS C 75 HIS C 79 0 SHEET 12 CA22 GLY C 41 VAL C 44 1 O LEU C 42 N ILE C 77 SHEET 13 CA22 ALA C 102 VAL C 106 0 SHEET 14 CA22 LYS C 75 HIS C 79 1 O ALA C 78 N SER C 104 SHEET 15 CA22 MET C 134 ASN C 138 0 SHEET 16 CA22 ALA C 102 VAL C 106 1 O VAL C 103 N VAL C 135 SHEET 17 CA22 VAL C 161 GLN C 166 0 SHEET 18 CA22 MET C 134 ASN C 138 1 O MET C 134 N GLY C 162 SHEET 19 CA22 VAL C 185 ASN C 188 0 SHEET 20 CA22 VAL C 161 GLN C 166 1 O GLY C 162 N VAL C 185 SHEET 21 CA22 GLY C 204 GLY C 207 0 SHEET 22 CA22 VAL C 8 ALA C 11 1 O MET C 9 N GLY C 207 SHEET 1 DA16 VAL D 8 ALA D 11 0 SHEET 2 DA16 GLY D 204 GLY D 207 1 O GLY D 205 N MET D 9 SHEET 3 DA16 GLY D 41 VAL D 44 0 SHEET 4 DA16 VAL D 8 ALA D 11 1 O ALA D 10 N TYR D 43 SHEET 5 DA16 LYS D 75 HIS D 79 0 SHEET 6 DA16 GLY D 41 VAL D 44 1 O LEU D 42 N ILE D 77 SHEET 7 DA16 ALA D 102 VAL D 106 0 SHEET 8 DA16 LYS D 75 HIS D 79 1 O ALA D 78 N SER D 104 SHEET 9 DA16 MET D 134 ASN D 138 0 SHEET 10 DA16 ALA D 102 VAL D 106 1 O VAL D 103 N VAL D 135 SHEET 11 DA16 VAL D 161 GLN D 166 0 SHEET 12 DA16 MET D 134 ASN D 138 1 O MET D 134 N GLY D 162 SHEET 13 DA16 VAL D 185 ASN D 188 0 SHEET 14 DA16 VAL D 161 GLN D 166 1 O GLY D 162 N VAL D 185 SHEET 15 DA16 GLY D 204 GLY D 207 0 SHEET 16 DA16 VAL D 8 ALA D 11 1 O MET D 9 N GLY D 207 LINK NZ LYS A 165 C2 3PY A 802 1555 1555 1.48 LINK NZ LYS B 165 C2 3PY B 804 1555 1555 1.47 LINK NZ LYS C 165 C2 3PY C 806 1555 1555 1.48 LINK NZ LYS D 165 C2 3PY D 808 1555 1555 1.48 CISPEP 1 LYS A 272 PRO A 273 0 1.35 CISPEP 2 LYS B 272 PRO B 273 0 0.97 CISPEP 3 LYS C 272 PRO C 273 0 0.76 CISPEP 4 LYS D 272 PRO D 273 0 1.13 SITE 1 AC1 8 ALA A 11 TYR A 43 GLY A 46 SER A 47 SITE 2 AC1 8 THR A 48 TYR A 137 LYS A 165 THR A 167 SITE 1 AC2 8 ALA B 11 TYR B 43 GLY B 46 SER B 47 SITE 2 AC2 8 THR B 48 TYR B 137 LYS B 165 THR B 167 SITE 1 AC3 7 ALA C 11 TYR C 43 GLY C 46 SER C 47 SITE 2 AC3 7 THR C 48 TYR C 137 LYS C 165 SITE 1 AC4 8 ALA D 11 TYR D 43 GLY D 46 SER D 47 SITE 2 AC4 8 THR D 48 TYR D 137 LYS D 165 THR D 167 CRYST1 83.740 95.990 89.650 90.00 115.16 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011942 0.000000 0.005609 0.00000 SCALE2 0.000000 0.010418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012324 0.00000