1EUX - Header Asymmetric Unit

HEADER HYDROLASE/HYDROLASE INHIBITOR 18-APR-00 1EUX

TITLE MODEL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH TITLE 2 E-64C

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CARICAIN); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAPAYA PROTEINASE, PROTEASE OMEGA; COMPND 5 EC: 3.4.22.30; COMPND 6 MUTATION: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA

KEYWDS CYSTEINE PROTEINASE, THIOL PROTEASE, HYDROLASE

EXPDTA THEORETICAL MODEL

AUTHOR S.BHATTACHARYA,A.BANERJEE

REVDAT 1 28-JUN-00 1EUX 0

JRNL AUTH S.BHATTACHARYA,A.PAL,A.BERA,S.CHAKRABORTY, JRNL AUTH 2 A.BANERJEE JRNL TITL THEORETICAL MODEL STRUCTURE OF A CARICAIN D158E JRNL TITL 2 MUTANT IN COMPLEX WITH E-64C JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.A.KATERELOS,M.A.TAYLOR,M.SCOTT,P.W.GOODENOUGH, REMARK 1 AUTH 2 R.W.PICKERSGILL REMARK 1 TITL CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN REMARK 1 TITL 2 COMPLEX WITH E-64 REMARK 1 REF FEBS LETT. V. 392 35 1996 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.YAMAMOTO,K.MATSUMOTO,H.OHISHI,T.ISHIDA,M.INOUE, REMARK 1 AUTH 2 K.KITAMURA,H.MIZUNO REMARK 1 TITL REFINED X-RAY STRUCTURE OF PAPAIN(DOT)E-64-C REMARK 1 TITL 2 COMPLEX AT 2.1-ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 266 14771 1991 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.MATSUMOTO,D.YAMAMOTO,H.OHISHI,K.TOMOO,T.ISHIDA, REMARK 1 AUTH 2 M.INOUE,T.SADATOME,K.KITAMURA,H.MIZUNO REMARK 1 TITL MODE OF BINDING OF E-64-C, A POTENT THIOL PROTEASE REMARK 1 TITL 2 INHIBITOR, TO PAPAIN AS DETERMINED BY X-RAY REMARK 1 TITL 3 CRYSTAL ANALYSIS OF THE COMPLEX REMARK 1 REF FEBS LETT. V. 245 171 1989 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.YAMAMOTO,K.MATSUMOTO,H.OHISHI,T.ISHIDA,M.INOUE, REMARK 1 AUTH 2 K.KITAMURA,H.MIZUNO REMARK 1 TITL THE IMPORTANCE OF VAL-157 HYDROPHOBIC INTERACTION REMARK 1 TITL 2 FOR PAPAIN INHIBITORY ACTIVITY OF AN EPOXYSUCCINYL REMARK 1 TITL 3 AMINO ACID DERIVATIVE; A STRUCTURE-ACTIVITY REMARK 1 TITL 4 RELATIONSHIP BASED ON THE CRYSTAL STRUCTURE OF THE REMARK 1 TITL 5 PAPAIN-E-64-C COMPLEX REMARK 1 REF FEBS LETT. V. 253 134 1990 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.-J.KIM,D.YAMAMOTO,K.MATSUMOTO,M.INOUE,T.ISHIDA, REMARK 1 AUTH 2 H.MIZUNO,S.SUMIYA,K.KITAMURA REMARK 1 TITL CRYSTAL STRUCTURE OF PAPAIN-E64-C COMPLEX. BINDING REMARK 1 TITL 2 DIVERSITY OF E64-C TO PAPAIN S=2= AND S=3= SUBSITES REMARK 1 REF BIOCHEM.J. V. 287 797 1992 REMARK 1 REFN ASTM BIJOAK UK ISSN 0306-3275

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1EUX COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 5 REMARK 5 RECENTLY POTENTIAL CYSTEIN PROTEASE INHIBITORS/ADDUCTS ARE REMARK 5 IN THE FOCUS FOR THEIR IMPORTANT APPLICATION IN MEDICAL REMARK 5 AND INDUSTRIAL SECTORS. A CLASS OF DRUGS WITH EXCELLENT REMARK 5 MECHANISM FOR FIGHTING DISEASES HAS BREATHED HOPE INTO REMARK 5 MEDICAL RESEARCH. THESE DRUGS,PROTEASE INHIBITORS, ARE REMARK 5 BEING USED AGAINST EVERYTHING FROM INFECTION, COMMON COLD, REMARK 5 INFLAMMATIONS IN ARTHRITIS TO AIDS AND EVEN IN CANCER. REMARK 5 IN ABSENCE OF ANY EXPERIMENTAL STRUCTURAL DATA FOR REMARK 5 E-64C COMPLEXED WITH CARICAIN,MOLECULAR MODELLING REMARK 5 HAS BEEN USED TO IDENTIFY CONSERVED SIGNATURES OF REMARK 5 BIOLOGICALLY IMPORTANT CONFORMATIONS AND MOTIFS, REMARK 5 RELEVANT IN BIOLOGICAL FUNCTIONS.

REMARK 6 REMARK 6 E6C IS (2S,3S)-3-(1-(N-(3-METHYLBUTYL)AMINO)-LEUCYLCARBOXYL) REMARK 6 OXIRANE-2-CARBOXYLATE.THIS COMPOUND WAS DESIGNED FROM THE REMARK 6 NATURAL PRODUCT E-64.E-64-C CONSISTS OF L-TRANSEPOXYSUCCINYL REMARK 6 L-LEUCYL, AND ISOAMYLAMIDE MOIETIES.

REMARK 7 REMARK 7 AS A PART OF A MAJOR PROGRAMME OF RESEARCH FOR REMARK 7 UNDERSTANDING SUBSTRATE SPECIFICITY OF THIOL PROTEASES, REMARK 7 WE HAVE TAKEN THE X-RAY CRYSTALLOGRAPHICALLY SOLVED REMARK 7 STRUCTURE OF CARICAIN(PDB CODE:1MEG,SOLVED AT 2.00 REMARK 7 RESOLUTION), A THIOL PROTEASE AND INHIBITOR E-64C REMARK 7 (FROM PAPAIN-E64C COMPLEX,PDB CODE:1PE6) AND DOCKED REMARK 7 THE INHIBITOR TO THE SUBSTRATE BINDING SITE OF THE REMARK 7 CARICAIN TO VISUALISE THE CONSERVED SIGNATURES OF REMARK 7 BIOLOGICALLY IMPORTANT CONFORMATIONS AND MOTIFS.IT HAS REMARK 7 BEEN REPORTED THAT THE MOLECULAR SURFACE OF BOTH THE REMARK 7 RECEPTOR AND INHIBITOR AT ACTIVE SITE USUALLY FIT REMARK 7 TOGETHER IN A COMPLEMENTARY FASHION AND THE INTERFACE REMARK 7 OF THE PROTEASE SYSTEM IS NOT CONTINUUM, BUT A SET OF REMARK 7 DISTINCT SUBSITES WITH DIFFERENT TOPOGRAPHIES AND POLAR REMARK 7 ENVIRONMENTS USUALLY E-64 INTERACTS WITH THE SN REMARK 7 SUBSITES OF CYSTEINE PROTEASES. ALTHOUGH THE SN-PN (N=1-3) REMARK 7 INTERACTIONS OF THE INHIBITOR WITH THE MAIN CHAINS OF THE REMARK 7 ACTIVE SITE RESIDUES ARE SIMILAR IN RESPECTIVE COMPLEXES, REMARK 7 THE SIGNIFICANT DIFFERENCE IS OBSERVED IN THE SIDE CHAIN REMARK 7 INTERACTIONS OF S2-P2 AND S3-P3 PAIRS BECAUSE OF DIFFERENT REMARK 7 RESIDUES CONSTITUTING THE RESPECTIVE SUBSITES.

REMARK 8 REMARK 8 DIFFERENCE ACCESSIBLE SURFACE AREA (DASA) STUDY OF CARICAIN REMARK 8 WITH AND WITHOUT THE INHIBITOR (E-64C) SHOW THAT THE REMARK 8 RESIDUES AT THE ACTIVE SITE OF CARICAIN:GLU19,GLY66,GLY65 REMARK 8 GLY23,CYS25,GLU158,HIS159,ALA160 MAKES EITHER HYDROGEN BOND REMARK 8 INTERACTION OR VANDERWAAL CONTACTS WITH THE INHIBITORS AND REMARK 8 TRP26,TYR67,PRO68,VAL133,VAL157 SHOW HYDROPHOBIC INTERACTION REMARK 8 INHIBITOR INVOLVING S2 AND S3 SUBSITES.INTERACTION AT THE S2 REMARK 8 SUBSITES INVOLVES SIDE CHAINS OF THE RECEPTOR MAINLY. REMARK 8 DASA STUDY SUGGESTS HOW BINDING AFFINITY AND MOLECULAR REMARK 8 RECOGNITION AFFECT STRUCTURE-FUNCTION ACTIVITY OF THE SYSTEM REMARK 8 MOLECULAR CONFORMATION OF THE INHIBITOR (E-64C) FALL IN THE REMARK 8 ALLOWED REGION OF STEREOCHEMISTRY AND ALL THE CONFORMATIONS REMARK 8 CARICAIN EITHER FALL IN THE ALLOWED REGION OR IN THE REMARK 8 EXTENDED REMARK 8 ALLOWED REGION OF THE RAMACHANDRAN PLOT SIGNIFYING THAT THE REMARK 8 IS OF THE CORRECT AND SIMILAR CONFORMATION AS THOSE REPORTED REMARK 8 OTHER THIOL PROTEASE-INHIBITOR COMPLEXES.

REMARK 9 REMARK 9 MODEL BUILDING OF THE INHIBITOR (E-64C) IN COMPLEX REMARK 9 WITH CARICAIN WAS PERFORMED ON A SILICON GRAPHICS INDIGO REMARK 9 WORKSTATION USING THE COMMERCIAL SOFTWARE PACKAGE INSIGHT-II REMARK 9 (BIOSYM TECHNOLOGY, SAN DIEGO, CA).

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-2000. REMARK 100 THE RCSB ID CODE IS RCSB010913.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C7X RELATED DB: PDB REMARK 900 1C7X CONTAINS THE SAME PROTEIN COMPLEXED WITH E64C

DBREF 1EUX A 1 216 EMBL 22661 CAA49504 133 348

SEQADV 1EUX GLU A 158 EMBL 22661 ASP 290 CONFLICT SEQADV 1EUX THR A 214 EMBL 22661 ILE 346 CONFLICT

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 E6C A 217 22

HETNAM E6C N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-2- HETNAM 2 E6C METHYL-BUTANE

FORMUL 2 E6C C15 H28 N2 O5

HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 GLU A 57 1 9 HELIX 4 4 HIS A 61 CYS A 63 5 3 HELIX 5 5 TYR A 67 GLY A 79 1 13 HELIX 6 6 ASN A 117 GLN A 128 1 12 HELIX 7 7 GLY A 138 LEU A 143 1 6 HELIX 8 8 GLY A 202 LEU A 206 5 5

SHEET 1 A 5 ILE A 148 PHE A 149 0 SHEET 2 A 5 TYR A 190 LYS A 194 1 O ARG A 192 N PHE A 149 SHEET 3 A 5 LYS A 172 LYS A 178 -1 O ILE A 175 N ILE A 193 SHEET 4 A 5 HIS A 159 SER A 169 -1 O THR A 162 N LYS A 178 SHEET 5 A 5 VAL A 5 ASP A 6 -1 N VAL A 5 O TYR A 166 SHEET 1 B 5 ILE A 148 PHE A 149 0 SHEET 2 B 5 TYR A 190 LYS A 194 1 O ARG A 192 N PHE A 149 SHEET 3 B 5 LYS A 172 LYS A 178 -1 O ILE A 175 N ILE A 193 SHEET 4 B 5 HIS A 159 SER A 169 -1 O THR A 162 N LYS A 178 SHEET 5 B 5 VAL A 130 VAL A 134 -1 O VAL A 130 N ALA A 163 SHEET 1 C 2 ILE A 80 HIS A 81 0 SHEET 2 C 2 ILE A 104 VAL A 105 -1 N VAL A 105 O ILE A 80 SHEET 1 D 2 GLY A 109 ARG A 112 0 SHEET 2 D 2 TYR A 211 THR A 214 -1 O TYR A 212 N GLY A 111

SSBOND 1 CYS A 22 CYS A 63 SSBOND 2 CYS A 56 CYS A 95 SSBOND 3 CYS A 153 CYS A 204

LINK SG CYS A 25 C2 E6C A 217 LINK CG GLU A 158 C21 E6C A 217

CISPEP 1 GLY A 151 PRO A 152 0 -3.82

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 0.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 0.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 0.000000 0.00000