HEADER ISOMERASE 17-JUN-10 2KZH TITLE THREE-DIMENSIONAL STRUCTURE OF A TRUNCATED PHOSPHORIBOSYLANTHRANILATE TITLE 2 ISOMERASE (RESIDUES 255-384) FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRYPTOPHAN BIOSYNTHESIS PROTEIN TRPCF; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-(5'-PHOSPHO-RIBOSYL)ANTHRANILATE ISOMERASE, PRAI, TRPRAI; COMPND 5 EC: 5.3.1.24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: TRPC, B1262, JW1254; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PWP107 KEYWDS TIM-BARREL, TRYPTOPHAN BIOSYNTHESIS, PROTEIN EVOLUTION, SUBDOMAIN, KEYWDS 2 ISOMERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.SETIYAPUTRA,J.P.MACKAY,W.M.PATRICK REVDAT 4 14-JUN-23 2KZH 1 REMARK REVDAT 3 26-FEB-20 2KZH 1 REMARK SEQADV REVDAT 2 13-JUL-11 2KZH 1 JRNL REVDAT 1 09-MAR-11 2KZH 0 JRNL AUTH S.SETIYAPUTRA,J.P.MACKAY,W.M.PATRICK JRNL TITL THE STRUCTURE OF A TRUNCATED PHOSPHORIBOSYLANTHRANILATE JRNL TITL 2 ISOMERASE SUGGESTS A UNIFIED MODEL FOR EVOLUTION OF THE JRNL TITL 3 (BETA ALPHA)8 BARREL FOLD JRNL REF J.MOL.BIOL. V. 408 291 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21354426 JRNL DOI 10.1016/J.JMB.2011.02.048 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.M.PATRICK,J.M.BLACKBURN REMARK 1 TITL IN VITRO SELECTION AND CHARACTERIZATION OF A STABLE REMARK 1 TITL 2 SUBDOMAIN OF PHOSPHORIBOSYLANTHRANILATE ISOMERASE. REMARK 1 REF FEBS J. V. 272 3684 2005 REMARK 1 REFN ISSN 1742-464X REMARK 1 PMID 16008567 REMARK 1 DOI 10.1111/J.1742-4658.2005.04794.X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.0, CNS 1.21 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CARTESIAN MOLECULAR DYNAMICS REMARK 4 REMARK 4 2KZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000101767. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM TRPRAI-1, 20 MM HEPES-2, REMARK 210 100 MM SODIUM CHLORIDE-3, 1 MM REMARK 210 DTT-4, 0.1 MM DSS-5, 95% H2O/5% REMARK 210 D2O; 0.6-1.0 MM [U-99% 15N] REMARK 210 TRPRAI-6, 20 MM HEPES-7, 100 MM REMARK 210 SODIUM CHLORIDE-8, 1 MM DTT-9, REMARK 210 0.1 MM DSS-10, 95% H2O/5% D2O; REMARK 210 0.6-0.8 MM [U-98% 13C; U-98% 15N] REMARK 210 TRPRAI-11, 20 MM HEPES-12, 100 REMARK 210 MM SODIUM CHLORIDE-13, 1 MM DTT- REMARK 210 14, 0.1 MM DSS-15, 95% H2O/5% REMARK 210 D2O; 0.7 MM [U-98% 13C; U-98% REMARK 210 15N] TRPRAI-16, 20 MM HEPES-17, REMARK 210 100 MM SODIUM CHLORIDE-18, 1 MM REMARK 210 DTT-19, 0.1 MM DSS-20, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HNCO; 2D 1H-1H NOESY; 3D HBHA(CO) REMARK 210 NH; 3D H(CCO)NH; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 1H-13C NOESY AROMATIC; 3D HNHA; REMARK 210 3D 1H-15N TOCSY; 3D HN(CA)CO REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, TOPSPIN 2.1, SPARKY REMARK 210 3.113, TALOS TALOS+, CNS 1.21, REMARK 210 PROCHECKNMR 3.5.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 REMARK 465 HIS A 140 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 ASN A 4 25.83 -149.28 REMARK 500 1 ALA A 32 108.84 -49.69 REMARK 500 1 SER A 74 88.84 62.28 REMARK 500 1 ALA A 98 4.12 -69.14 REMARK 500 1 GLN A 129 114.32 69.30 REMARK 500 2 SER A 74 74.88 67.75 REMARK 500 2 LEU A 75 -168.40 -77.81 REMARK 500 2 ALA A 76 -52.39 -128.70 REMARK 500 2 GLU A 85 147.88 -179.50 REMARK 500 2 GLU A 116 -61.51 -132.07 REMARK 500 2 ALA A 132 117.65 68.58 REMARK 500 3 ASN A 4 29.75 -149.82 REMARK 500 3 PRO A 51 71.39 -68.12 REMARK 500 3 SER A 74 72.21 59.09 REMARK 500 3 ASN A 83 -24.84 -39.00 REMARK 500 3 GLU A 85 148.65 -175.11 REMARK 500 3 GLU A 116 -85.07 -103.30 REMARK 500 4 ASN A 4 28.50 -148.20 REMARK 500 4 SER A 74 73.29 52.32 REMARK 500 4 GLU A 85 135.45 -175.74 REMARK 500 4 GLU A 116 -58.75 -149.08 REMARK 500 5 GLU A 3 -75.49 -86.20 REMARK 500 5 LYS A 5 93.15 -47.22 REMARK 500 5 THR A 33 72.89 52.33 REMARK 500 5 PRO A 35 5.83 -65.67 REMARK 500 5 PRO A 51 45.02 -73.25 REMARK 500 5 HIS A 61 -74.65 -106.28 REMARK 500 5 SER A 107 107.28 -59.02 REMARK 500 5 GLU A 110 -73.93 -90.10 REMARK 500 5 ASP A 126 89.00 -66.95 REMARK 500 6 GLU A 3 111.05 68.54 REMARK 500 6 ASN A 4 37.90 -148.52 REMARK 500 6 ALA A 32 96.80 -43.86 REMARK 500 6 PRO A 35 19.90 -67.74 REMARK 500 6 PRO A 51 48.30 -76.06 REMARK 500 6 HIS A 61 -61.43 -107.93 REMARK 500 6 SER A 74 74.43 59.89 REMARK 500 6 GLU A 85 148.90 -176.88 REMARK 500 6 GLU A 116 -60.44 -134.87 REMARK 500 6 ASP A 126 102.74 -56.56 REMARK 500 7 ASN A 4 44.78 -153.28 REMARK 500 7 LYS A 5 96.20 -67.59 REMARK 500 7 LEU A 9 147.58 -172.29 REMARK 500 7 SER A 74 82.83 60.09 REMARK 500 7 GLU A 116 -68.62 -136.23 REMARK 500 8 LYS A 5 101.49 -51.03 REMARK 500 8 TYR A 25 -172.09 -170.60 REMARK 500 8 THR A 33 9.63 53.73 REMARK 500 8 PRO A 35 0.16 -67.32 REMARK 500 8 SER A 74 73.63 54.69 REMARK 500 REMARK 500 THIS ENTRY HAS 144 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 59 0.07 SIDE CHAIN REMARK 500 14 ARG A 93 0.08 SIDE CHAIN REMARK 500 15 ARG A 93 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PII RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE FULL-LENGTH PHOSPHORYBOSILANTHRANILATE REMARK 900 ISOMERASE (PRAI) FROM ESCHERICIA COLI REMARK 900 RELATED ID: 17005 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 132-134 ARE ACTUALLY RESIDUES FROM A LINKER THAT CONNECTS REMARK 999 THE MOLECULE TO THE HEXAHISTIDINE TAG DBREF 2KZH A 2 131 UNP P00909 TRPC_ECOLI 255 384 SEQADV 2KZH MET A 1 UNP P00909 INITIATING METHIONINE SEQADV 2KZH ALA A 132 UNP P00909 SEE REMARK 999 SEQADV 2KZH GLY A 133 UNP P00909 SEE REMARK 999 SEQADV 2KZH SER A 134 UNP P00909 SEE REMARK 999 SEQADV 2KZH HIS A 135 UNP P00909 EXPRESSION TAG SEQADV 2KZH HIS A 136 UNP P00909 EXPRESSION TAG SEQADV 2KZH HIS A 137 UNP P00909 EXPRESSION TAG SEQADV 2KZH HIS A 138 UNP P00909 EXPRESSION TAG SEQADV 2KZH HIS A 139 UNP P00909 EXPRESSION TAG SEQADV 2KZH HIS A 140 UNP P00909 EXPRESSION TAG SEQRES 1 A 140 MET GLY GLU ASN LYS VAL CYS GLY LEU THR ARG GLY GLN SEQRES 2 A 140 ASP ALA LYS ALA ALA TYR ASP ALA GLY ALA ILE TYR GLY SEQRES 3 A 140 GLY LEU ILE PHE VAL ALA THR SER PRO ARG CYS VAL ASN SEQRES 4 A 140 VAL GLU GLN ALA GLN GLU VAL MET ALA ALA ALA PRO LEU SEQRES 5 A 140 GLN TYR VAL GLY VAL PHE ARG ASN HIS ASP ILE ALA ASP SEQRES 6 A 140 VAL VAL ASP LYS ALA LYS VAL LEU SER LEU ALA ALA VAL SEQRES 7 A 140 GLN LEU HIS GLY ASN GLU GLU GLN LEU TYR ILE ASP THR SEQRES 8 A 140 LEU ARG GLU ALA LEU PRO ALA HIS VAL ALA ILE TRP LYS SEQRES 9 A 140 ALA LEU SER VAL GLY GLU THR LEU PRO ALA ARG GLU PHE SEQRES 10 A 140 GLN HIS VAL ASP LYS TYR VAL LEU ASP ASN GLY GLN GLY SEQRES 11 A 140 GLY ALA GLY SER HIS HIS HIS HIS HIS HIS HELIX 1 1 ARG A 11 GLY A 22 1 12 HELIX 2 2 ASN A 39 MET A 47 1 9 HELIX 3 3 ASP A 62 LEU A 73 1 12 HELIX 4 4 GLY A 82 GLU A 84 5 3 HELIX 5 5 GLN A 86 LEU A 96 1 11 SHEET 1 A 4 TYR A 54 PHE A 58 0 SHEET 2 A 4 ALA A 76 LEU A 80 1 O GLN A 79 N GLY A 56 SHEET 3 A 4 ALA A 101 LEU A 106 1 O TRP A 103 N VAL A 78 SHEET 4 A 4 LYS A 122 LEU A 125 1 O VAL A 124 N LEU A 106 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1