HEADER HYDROLASE 04-MAY-96 1MEG TITLE CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARICAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAPAYA PROTEINASE, PROTEASE OMEGA; COMPND 5 EC: 3.4.22.30; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: PET; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET VECTOR; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS CYSTEINE PROTEINASE, THIOL PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.A.KATERELOS REVDAT 3 03-NOV-21 1MEG 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1MEG 1 VERSN REVDAT 1 11-JAN-97 1MEG 0 JRNL AUTH N.A.KATERELOS,M.A.TAYLOR,M.SCOTT,P.W.GOODENOUGH, JRNL AUTH 2 R.W.PICKERSGILL JRNL TITL CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH JRNL TITL 2 E-64. JRNL REF FEBS LETT. V. 392 35 1996 JRNL REFN ISSN 0014-5793 JRNL PMID 8769310 JRNL DOI 10.1016/0014-5793(96)00697-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.KATERELOS,P.W.GOODENOUGH REMARK 1 TITL RAPID KINETICS STUDIES AND STRUCTURAL DETERMINATION OF A REMARK 1 TITL 2 CYSTEINE PROTEINASE MUTANT IMPLIES THAT RESIDUE ASP 158 IN REMARK 1 TITL 3 CARICAIN HAS A MAJOR EFFECT UPON THE ABILITY OF THE ACTIVE REMARK 1 TITL 4 SITE HISTIDINE TO PROTONATE A DIPYRIDYL PROBE REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 1 REFERENCE 2 REMARK 1 AUTH M.A.TAYLOR,K.C.BAKER,I.F.CONNERTON,N.J.CUMMINGS,G.W.HARRIS, REMARK 1 AUTH 2 I.M.HENDERSON,S.T.JONES,R.W.PICKERSGILL,I.G.SUMNER, REMARK 1 AUTH 3 J.WARWICKER,ET AL. REMARK 1 TITL AN UNEQUIVOCAL EXAMPLE OF CYSTEINE PROTEINASE ACTIVITY REMARK 1 TITL 2 AFFECTED BY MULTIPLE ELECTROSTATIC INTERACTIONS REMARK 1 REF PROTEIN ENG. V. 7 1267 1994 REMARK 1 REFN ISSN 0269-2139 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.F.REVELL,N.J.CUMMINGS,K.C.BAKER,M.E.COLLINS,M.A.TAYLOR, REMARK 1 AUTH 2 I.G.SUMNER,R.W.PICKERSGILL,I.F.CONNERTON,P.W.GOODENOUGH REMARK 1 TITL NUCLEOTIDE SEQUENCE AND EXPRESSION IN ESCHERICHIA COLI OF REMARK 1 TITL 2 CDNAS ENCODING PAPAYA PROTEINASE OMEGA FROM CARICA PAPAYA REMARK 1 REF GENE V. 127 221 1993 REMARK 1 REFN ISSN 0378-1119 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.A.TAYLOR,K.A.PRATT,D.F.REVELL,K.C.BAKER,I.G.SUMNER, REMARK 1 AUTH 2 P.W.GOODENOUGH REMARK 1 TITL ACTIVE PAPAIN RENATURED AND PROCESSED FROM INSOLUBLE REMARK 1 TITL 2 RECOMBINANT PROPAPAIN EXPRESSED IN ESCHERICHIA COLI REMARK 1 REF PROTEIN ENG. V. 5 455 1992 REMARK 1 REFN ISSN 0269-2139 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 11858 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 1642 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.15 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.740 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.56 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 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: REMARK 3 ATOMS C13, C14, C15, N3, C16, N4 AND N5 OF E64 WERE NOT REMARK 3 VISIBLE IN DENSITY BECAUSE OF THE HIGH MOBILITY OF THAT REMARK 3 PART OF THE E-64 MOLECULE WHICH ACCOUNTS FOR THEIR HIGH REMARK 3 TEMPERATURE FACTORS. REMARK 4 REMARK 4 1MEG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174974. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-94 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12010 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.72500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.66500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.72500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.66500 REMARK 290 SMTRY3 4 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: 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 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 GLU A 158 9.86 -157.63 REMARK 500 SER A 209 102.56 -168.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ACTIVE SITE. REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E64 A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EOH A 218 DBREF 1MEG A 1 216 UNP P10056 PAPA3_CARPA 133 348 SEQADV 1MEG GLU A 158 UNP P10056 ASP 290 ENGINEERED MUTATION SEQRES 1 A 216 LEU PRO GLU ASN VAL ASP TRP ARG LYS LYS GLY ALA VAL SEQRES 2 A 216 THR PRO VAL ARG HIS GLN GLY SER CYS GLY SER CYS TRP SEQRES 3 A 216 ALA PHE SER ALA VAL ALA THR VAL GLU GLY ILE ASN LYS SEQRES 4 A 216 ILE ARG THR GLY LYS LEU VAL GLU LEU SER GLU GLN GLU SEQRES 5 A 216 LEU VAL ASP CYS GLU ARG ARG SER HIS GLY CYS LYS GLY SEQRES 6 A 216 GLY TYR PRO PRO TYR ALA LEU GLU TYR VAL ALA LYS ASN SEQRES 7 A 216 GLY ILE HIS LEU ARG SER LYS TYR PRO TYR LYS ALA LYS SEQRES 8 A 216 GLN GLY THR CYS ARG ALA LYS GLN VAL GLY GLY PRO ILE SEQRES 9 A 216 VAL LYS THR SER GLY VAL GLY ARG VAL GLN PRO ASN ASN SEQRES 10 A 216 GLU GLY ASN LEU LEU ASN ALA ILE ALA LYS GLN PRO VAL SEQRES 11 A 216 SER VAL VAL VAL GLU SER LYS GLY ARG PRO PHE GLN LEU SEQRES 12 A 216 TYR LYS GLY GLY ILE PHE GLU GLY PRO CYS GLY THR LYS SEQRES 13 A 216 VAL GLU HIS ALA VAL THR ALA VAL GLY TYR GLY LYS SER SEQRES 14 A 216 GLY GLY LYS GLY TYR ILE LEU ILE LYS ASN SER TRP GLY SEQRES 15 A 216 THR ALA TRP GLY GLU LYS GLY TYR ILE ARG ILE LYS ARG SEQRES 16 A 216 ALA PRO GLY ASN SER PRO GLY VAL CYS GLY LEU TYR LYS SEQRES 17 A 216 SER SER TYR TYR PRO THR LYS ASN HET E64 A 217 25 HET EOH A 218 3 HETNAM E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO- HETNAM 2 E64 BUTYL]-GUANIDINE HETNAM EOH ETHANOL FORMUL 2 E64 C15 H30 N5 O5 1+ FORMUL 3 EOH C2 H6 O FORMUL 4 HOH *94(H2 O) HELIX 1 1 CYS A 25 THR A 42 1 18 HELIX 2 2 GLU A 50 CYS A 56 1 7 HELIX 3 3 GLY A 62 LYS A 64 5 3 HELIX 4 4 PRO A 68 ASN A 78 1 11 HELIX 5 5 GLU A 118 LYS A 127 1 10 HELIX 6 6 ARG A 139 GLN A 142 1 4 HELIX 7 7 VAL A 203 GLY A 205 5 3 SHEET 1 A 2 GLY A 109 ARG A 112 0 SHEET 2 A 2 TYR A 211 THR A 214 -1 N THR A 214 O GLY A 109 SHEET 1 B 4 VAL A 130 VAL A 134 0 SHEET 2 B 4 HIS A 159 SER A 169 -1 N ALA A 163 O VAL A 130 SHEET 3 B 4 LYS A 172 LYS A 178 -1 N LYS A 178 O THR A 162 SHEET 4 B 4 TYR A 190 LYS A 194 -1 N ILE A 193 O ILE A 175 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.03 SSBOND 3 CYS A 153 CYS A 204 1555 1555 2.03 LINK SG CYS A 25 C2 E64 A 217 1555 1555 1.83 CISPEP 1 GLY A 151 PRO A 152 0 -3.81 SITE 1 ACT 2 CYS A 25 HIS A 159 SITE 1 AC1 12 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 12 TRP A 26 GLY A 65 GLY A 66 TYR A 67 SITE 3 AC1 12 VAL A 133 GLU A 158 HIS A 159 HOH A 310 SITE 1 AC2 4 HIS A 18 GLY A 20 ALA A 90 HOH A 312 CRYST1 53.450 65.330 64.370 90.00 111.60 90.00 C 1 2 1 4 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 0.018709 0.000000 0.007407 0.00000 SCALE2 0.000000 0.015307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016709 0.00000