HEADER HYDROLASE/HYDROLASE INHIBITOR 19-MAY-00 1F1I TITLE MODEL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH TITLE 2 LEUPEPTIN (ACETYL-L-LEUCYL-L-LEUCYL-L-ARGINAL) 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 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LEUPEPTIN; COMPND 9 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 SECRETION: LATEX; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ACTINOMYCETES; SOURCE 7 ORGANISM_COMMON: BACTERIA KEYWDS CYSTEINE PROTEINASE INHIBITOR, THIOL PROTEASE INHIBITOR, KEYWDS 2 HYDROLASE EXPDTA THEORETICAL MODEL AUTHOR S.BHATTACHARYYA,A.BANERJEE REVDAT 1 05-JUL-00 1F1I 0 JRNL AUTH S.BHATTACHARYYA,A.PAL,A.BERA,S.CHAKRABORTY,S.GHOSH, JRNL AUTH 2 A.BANERJEE JRNL TITL THEORETICAL MODEL STRUCTURE OF A CARICAIN D158E JRNL TITL 2 MUTANT COMPLEX WITH DIFFERENT BIOLOGICALLY JRNL TITL 3 IMPORTANT INHIBITORS 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 E.SCHROEDER,C.PHILLIPS,E.GARMAN,K.HARLOS,C.CRAWFORD REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STRUCTURE OF A REMARK 1 TITL 2 PAPAIN-LEUPEPTIN COMPLEX REMARK 1 REF FEBS LETT. V. 315 38 1993 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 3 REMARK 1 AUTH R.M.SCHULTZ,P.VARMA-NELSON,R.ORTIZ,K.A.KOZLOWSKI, REMARK 1 AUTH 2 A.T.ORAWSKI,P.PAGAST,A.FRANKFATER REMARK 1 TITL ACTIVE AND INACTIVE FORMS OF THE TRANSITION-STATE REMARK 1 TITL 2 ANALOG PROTEASE INHIBITOR LEUPEPTIN: EXPLANATION REMARK 1 TITL 3 OF THE OBSERVED SLOW BINDING OF LEUPEPTIN TO REMARK 1 TITL 4 CATHEPSIN B AND PAPAIN. REMARK 1 REF J.BIOL.CHEM. V. 264 1497 1989 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER INSIGHT-II, BIOSYM TECHNOLOGY, SAN REMARK 3 DIEGO, CA, 95.0 REMARK 3 AUTHORS : BIOSYM TECHNOLOGY INC(MSI) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1F1I COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 7 REMARK 7 RECENTLY POTENTIAL CYSTEINE PROTEASE INHIBITORS/ADDUCTS REMARK 7 ARE IN THE FOCUS FOR THEIR IMPORTANT APPLICATION REMARK 7 IN MEDICAL AND INDUSTRIAL SECTORS. REMARK 7 REMARK 7 A CLASS OF DRUGS WITH EXCELLENT MECHANISM FOR FIGHTING REMARK 7 DISEASES HAS BREATHED HOPE INTO MEDICAL RESEARCH. THESE REMARK 7 DRUGS, PROTEASE INHIBITORS, ARE BEING USED AGAINST REMARK 7 EVERYTHING FROM INFECTION, COMMON COLD, INFLAMMATIONS IN REMARK 7 ARTHRITIS TO AIDS AND EVEN IN CANCER. REMARK 7 REMARK 7 IN ABSENCE OF ANY EXPERIMENTAL STRUCTURAL DATA REMARK 7 FOR LEUPEPTIN COMPLEXED WITH CARICAIN, REMARK 7 MOLECULAR MODELLING HAS BEEN USED TO IDENTIFY REMARK 7 CONSERVED SIGNATURES OF BIOLOGICALLY IMPORTANT REMARK 7 CONFORMATIONS AND MOTIFS, RELEVANT IN BIOLOGICAL REMARK 7 FUNCTIONS. PEPTIDE ARGINAL (ARGININE ALDEHYDE) PROTEINASE REMARK 7 INHIBITORS SUCH AS LEUPEPTIN AND ANTIPAIN WERE REMARK 7 ORIGINALLY DISCOVERED BY BY UMEZAWA(1976) AND CO-WORKERS REMARK 7 IN CULTURES OF ACTINOMYCETES BACTERIA AND HAVE BEEN REMARK 7 WIDELY USED IN THE STUDY OF THE ROLES OF IMPORTANT SERINE REMARK 7 AND CYSTEINE TYPE ARGININE-SPECIFIC PROTEASES. REMARK 7 REMARK 7 LEUPEPTINS GENERALLY BIND TO THE SERINE AND CYSTEINE REMARK 7 PROTEASES AS HEMIACETALS OR THIOHEMIACETALS WHICH MIMIC REMARK 7 THE STRUCTURE OF REACTION TRANSITION STATES. LEUPEPTIN REMARK 7 HAS BEEN USED TO INVESTIGATE THE POSSIBLE ROLE OF REMARK 7 PROTEASES IN TUMOR CELL INVASION AND METASTASIS, PROTEIN REMARK 7 SYNTHESIS AND MUSCULAR DISTROPHY. REMARK 7 REMARK 7 AS A PART OF A MAJOR PROGRAM OF RESEARCH REMARK 7 FOR UNDERSTANDING SUBSTRATE SPECIFICITY OF THIOL REMARK 7 PROTEASES, WE HAVE TAKEN THE X-RAY CRYSTALLOGRAPHICALLY REMARK 7 SOLVED STRUCTURE OF CARICAIN (PDB CODE 1MEG, SOLVED AT REMARK 7 2.00 A RESOLUTION), A THIOL PROTEASE REMARK 7 AND THE SUBSTRATE-LIKE INHIBITOR LEUPEPTIN (FROM REMARK 7 LEUPEPTIN-PAPAIN COMPLEX, PDB CODE 1POP) AND DOCKED THE REMARK 7 INHIBITOR TO THE SUBSTRATE BINDING SITE OF CARICAIN TO REMARK 7 VISUALIZE CONSERVED SIGNATURES OF BIOLOGICALLY IMPORTANT REMARK 7 CONFORMATIONS AND MOTIFS.IT HAS BEEN REPORTED THAT REMARK 7 MOLECULAR SURFACE OF BOTH THE RECEPTOR AND INHIBITOR AT REMARK 7 ACTIVE SITE USUALLY FIT TOGATHER IN A COMPLEMENTARY REMARK 7 FASHION AND THE INTERFACE OF THE PROTEASE SYSTEM IS NOT REMARK 7 CONTINUUM, BUT A SET OF DISTINCT SUBSITES WITH DIFFERENT REMARK 7 TOPOGRAPHIES AND POLAR ENVIRONMENTS FOR STUDYING REMARK 7 STRUCTURE-FUNCTION RELATIONSHIPS ON THE STRUCTURAL BASIS. REMARK 7 REMARK 7 DIFFERENCE ACCESSIBLE SURFACE AREA (DASA) STUDY OF REMARK 7 CARICAIN WITH AND WITHOUT THE INHIBITOR (LEUPEPTIN) SHOW REMARK 7 THAT THE RESIDUES AT THE ACTIVE SITE OF CARICAIN (GLU19, REMARK 7 LYS66, GLY65, LYS23, CYS25, TRP26, TYR67, PRO68, VAL133, REMARK 7 VAL157, GLU158, HIS159, ALA160, LYS64) INTERACT WITH THE REMARK 7 INHIBITOR. REMARK 7 REMARK 7 DASA STUDY SUGGESTS HOW BINDING AFFINITY AND REMARK 7 MOLECULAR RECOGNITION AFFECT STRUCTURE-FUNCTION ACTIVITY REMARK 7 OF THE SYSTEM MOLECULAR CONFORMATION OF THE INHIBITOR REMARK 7 (LEUPEPTIN) FALL IN ALLOWED REGION OF STEREOCHEMISTRY AND REMARK 7 ALL THE CONFORMATIONS CARICAIN EITHER FALL IN THE ALLOWED REMARK 7 REGION OR IN THE EXTENDED ALLOWED REGION OF THE REMARK 7 RAMACHANDRAN PLOT SIGNIFYING THAT THE COMPLEX IS OF THE REMARK 7 CORRECT AND SIMILAR CONFORMATION AS THAT OF REPORTED REMARK 7 OTHER THIOL PROTEASE-INHIBITOR COMPLEXES. REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-2000. REMARK 100 THE RCSB ID CODE IS RCSB011128. 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 CARICAIN COMPLEXED WITH ZPACK REMARK 900 RELATED ID: 1EUX RELATED DB: PDB REMARK 900 1EUX CONTAINS THE SAME PROTEIN COMPLEXED WITH E64C DBREF 1F1I A 1 216 UNP P10056 PAP3_CARPA 133 348 SEQADV 1F1I GLU A 158 UNP P10056 ASP 290 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 SEQRES 1 B 4 ACE LEU LEU ARG HET ACE B 300 3 HETNAM ACE ACETYL GROUP FORMUL 2 ACE C2 H4 O 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 C ARG B 303 CISPEP 1 GLY A 151 PRO A 152 0 -3.75 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 MASTER 117 0 1 8 14 0 0 6 0 0 0 18 END