HEADER HYDROLASE 08-JUN-04 1W0Q TITLE A THREE DIMENSIONAL STRUCTURAL MODEL OF STEM BROMELAIN: A TITLE 2 CRITICAL COMPARATIVE ANALYSIS OF GLYCOSYLATION TOWARDS TITLE 3 FUNCTIONAL AND STRUCTURAL STABILITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMELAIN; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: GLYCOSYL CHAIN OF STEM BROMELAIN; COMPND 5 EC: 3.4.22.32; COMPND 6 OTHER_DETAILS: BRANCHED HETERO OLIGOSACHHARIDE CHAIN COMPND 7 (CCSD:42165) CONTAINING NAG, MANNOSE, XYLOSE AND FUCOSE IN COMPND 8 2:2:1:1 RATIO N-LINKED AT ASPARAGINE 117 OF STEM BROMELAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ANANUS COMOSUS; SOURCE 3 ORGANISM_COMMON: PINEAPPLE; SOURCE 4 TISSUE: STEM; SOURCE 5 OTHER_DETAILS: THIS IS A PLANT FROM BROMELIACEAE FAMILY KEYWDS HYDROLASE,THIOL PROTEASE,GLYCOPROTEIN,STEM BROMELAIN EXPDTA THEORETICAL MODEL AUTHOR N.BANERJEE,S.DAS,A.BANERJEE REVDAT 1 25-JAN-06 1W0Q 0 JRNL AUTH N.BANERJEE,A.BANERJEE JRNL TITL A THREE DIMENSIONAL STRUCTURAL MODEL OF STEM JRNL TITL 2 BROMELAIN: A CRITICAL COMPARATIVE ANALYSIS OF JRNL TITL 3 GLYCOSYLATION TOWARDS FUNCTIONAL AND STRUCTURAL JRNL TITL 4 STABILITY JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.VAN KUIK,R.A.HOFFMANN,J.H.G.M.MUTSAERS, REMARK 1 AUTH 2 H.VAN HALBEEK,J.P.KAMERLING,J.F.G.VLIEGENTHART REMARK 1 TITL A 500-MHZ 1H-NMR STUDY ON THE N-LINKED REMARK 1 TITL 2 CARBOHYDRATE CHAIN OF BROMELAIN. 1H-NMR REMARK 1 TITL 3 STRUCTURAL-REPORTER-GROUPS OF FUCOSE REMARK 1 TITL 4 ALPHA(1-3)-LINKED TO ASPARAGINE-BOUND REMARK 1 TITL 5 N-ACETYLGLUCOSAMINE REMARK 1 REF GLYCOCONJ. J. V. 3 27 1986 REMARK 1 REFN ISSN 0282-0080 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.RITONJA,A.D.ROWAN,D.J.BUTTLE,N.D.RAWLINGS,V.TURK, REMARK 1 AUTH 2 A.J.BARRETT REMARK 1 TITL STEM BROMELAIN: AMINO ACID SEQUENCE AND REMARK 1 TITL 2 IMPLICATION FOR WEAK BINDING OF CYSTATIN. REMARK 1 REF FEBS LETT. V. 247 419 1989 REMARK 1 REFN ASTM FEBLAL NE ISSN 0014-5793 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.BISWAS,C.CHAKRABARTI,S.KUNDU,M.V.JAGANNADHAM, REMARK 1 AUTH 2 J.K.DATTAGUPTA REMARK 1 TITL PROPOSED AMINO ACID SEQUENCE AND THE 1.63 A X-RAY REMARK 1 TITL 2 CRYSTAL STRUCTURE OF A PLANT CYSTEINE ERVATAMIN B: REMARK 1 TITL 3 SOME INSIGHTS INTO THE STRUCTURAL BASI PROTEASE, REMARK 1 TITL 4 OF ITS STABILITY AND SUBSTRATE SPECIFICIT REMARK 1 REF PROTEINS: STRUCT.,FUNCT., V. 51 489 2003 REMARK 1 REF 2 GENET. REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 1 REFERENCE 4 REMARK 1 AUTH K.H.CHOI,R.A.LAURSEN,K.N.ALLEN REMARK 1 TITL THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE REMARK 1 TITL 2 WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, REMARK 1 TITL 3 ZINGIBER OFFICINALE REMARK 1 REF BIOCHEMISTRY V. 38 11624 1999 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 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: MOLECULAR MODELLING HAS BEEN USED TO REMARK 3 BUILD THE UNKNOWN PROTEIN REMARK 4 REMARK 4 1W0Q COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 10-JUN-2004. REMARK 100 THE EBI ID CODE IS EBI-20118. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: STRUCTURE OF STEM BROMELAIN, A THIOL PROTEASE OF REMARK 220 EXTREME BIOLOGICAL IMPORTANCE TO IDENTIFY CONSERVED REMARK 220 SIGNATURES OF BIOLOGICALLY IMPORTANT CONFORMATIONS AND REMARK 220 MOTIFS RELEVANT IN BIOLOGICAL FUNCTIONS. BIOLOGICAL REMARK 220 SIGNIFICANCE OF CARBOHYDRATE MOIETY OF A GLYCOPROTEIN REMARK 220 HAS BEEN A MATTER OF MUCH SPECULATION. STEM BROMELAIN IS REMARK 220 A THIOL PROTEASE, WHICH CONTAINS A, SINGLE HETERO- REMARK 220 OLIGOSACCHARIDE UNIT PER MOLECULES. DEGLYCOSYLATED REMARK 220 BROMELAIN SHOWED DECREASED ENZYMATIC ACTIVITY AND THUS REMARK 220 IT IS PROBABLE THAT GLYCOSYLATION CONTRIBUTES TOWARDS REMARK 220 FUNCTIONAL STABILITY OF THE GLYCOENZYME.THE HIGHLY REMARK 220 BRANCHED OLIGOSACCHARIDE GROUP CONSISTS OF D- REMARK 220 GLUCOSAMINE,D-MANOSE,D-XYLOSE, AND L-FRUCTOSE IN RATIOS REMARK 220 OF 2:2:1:1. AS A PART OF A MAJOR PROGRAMME OF RESEARCH REMARK 220 FOR UNDERSTANDING SUBSTRATE SPECIFICITY OF THIOL REMARK 220 PROTEASES, WE HAVE TAKEN THE X-RAY SOLVED STRUCTURE OF REMARK 220 ERVATAMIN (PDB CODE: 1IWD,SOLVED AT 1.63A RESOLUTION),A REMARK 220 THIOL PROTEASE AND DID THE KNOWLEDGE BASE MODELING OF REMARK 220 THE GLYCOSYL FROM (GINGER PROTEASE, GPII (PDB CODE: REMARK 220 1CQD) AND ABRIN (PDB CODE: 1ABR) AND DOCKED THE GLYCOSYL REMARK 220 PART TO THE N-LINKED ASN 117 RESIDUE OF STEM BROMELAIN REMARK 220 AND MINIMIZED TO VISUALISE THE CONSERVED SIGNATURES OF REMARK 220 BIOLOGICALLY IMPORTANT CONFORMATIONS AND MOTIFS. ALL REMARK 220 MOLECULAR CONFORMATIONS OF THE STEM BROMELAIN STRUCTURE REMARK 220 FALL EITHER IN THE ALLOWED REGION OF STEREOCHEMISTRY OR REMARK 220 IN THE EXTENDED ALLOWED REGION OF THE RAMACHANDRAN PLOT REMARK 220 SIGNIFYING THAT THE PROTEIN IS OF THE CORRECT AND REMARK 220 SIMILAR CONFORMATIONS AS THAT OF REPORTED OTHER THIOL REMARK 220 PROTEASE STRUCTURES. KNOWLEDGE-BASED MODEL BUILDING OF REMARK 220 GLYCOSYLATED STEM BROMELAIN WAS PERFORMED ON A SILICON REMARK 220 GRAPHICS INDIGO WORKSTATION USING THE COMMERCIAL REMARK 220 SOFTWARE PACKAGE INSIGHT-II (BIOSYM TECHNOLOGY,SAN REMARK 220 DIEGO, CA). 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 400 REMARK 400 COMPOUND REMARK 400 RECENTLY POTENTIAL CYSTEIN PROTEASES ARE IN THE FOCUS REMARK 400 FOR THEIR IMPORTANCE IN MEDICAL AND INDUSTRIAL SECTORS. REMARK 400 STEM BROMELAIN IS A CYSTEINE PROTEASE FROM REMARK 400 ANANUS COMOSUS TO PAPAIN FAMILY. THE ENZYME IS A 212 REMARK 400 AMINO ACID GLYCOPROTEIN POSSESSING ONE N-LINKED REMARK 400 OLIGOSACCHARIDE CHAIN (2% GLYCOSYLATED BY WEIGHT) AT REMARK 400 ASN 117. THE SEQUENCE OF STEM BROMELAIN IS KNOWN BUT NO REMARK 400 CRYSTAL STRUCTURE IS KNOWN YET. THE SEQUENCE HOMOLOGY OF REMARK 400 STEM BROMELAIN IS AROUND 47% WITH ERVATAMINB OF PAPAIN REMARK 400 FAMILY. A MODEL OF STEM BROMELAIN HAS BEEN CONSTRUCTED REMARK 400 BASED ON HOMOLOGY MODELING AND MOLECULAR DYNAMIC REMARK 400 SIMULATIONS. STRUCTURAL BASIC FEATURES OF THE PROTEIN IS REMARK 400 SIMILAR TO THOSE OF HOMOLOGOUS PROTEASES OF THE PAPAIN REMARK 400 FAMILY, FOLDING INTO TWO DISTINCT LEFT AND RIGHT DOMAINS REMARK 400 SEPARATED BY AN ACTIVE SITE CLEFT. THE N-LINKED GLYCOSYL REMARK 400 CHAIN PARTICIPATES IN INTER-ACTION VIA HYDROGEN BONDS REMARK 400 FOR TETHERING THE PROTEIN WITH THE CARBOHYDRATE MOIETY REMARK 400 WITHOUT INTERVENING ORDERED WATER MOLECULE. 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 SER B 194 CB - CA - C ANGL. DEV. = 18.6 DEGREES REMARK 500 SER B 196 N - CA - C ANGL. DEV. = 18.9 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 VAL B 192 157.83 53.05 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY B 60 TYR B 61 144.90 REMARK 500 THR B 98 ASP B 99 -145.01 REMARK 500 VAL B 101 PRO B 102 149.88 REMARK 500 ALA B 178 LYS B 179 -60.97 REMARK 500 ASP B 191 VAL B 192 82.62 REMARK 500 SER B 194 SER B 195 37.01 REMARK 500 SER B 195 SER B 196 111.41 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: XYZ REMARK 800 SITE_DESCRIPTION: XYZ BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: RAM REMARK 800 SITE_DESCRIPTION: RAM BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: NDG REMARK 800 SITE_DESCRIPTION: NDG BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: NGZ REMARK 800 SITE_DESCRIPTION: NGZ BINDING SITE FOR CHAIN B DBREF 1W0Q B 2 211 UNP P14518 BROM2_ANACO 2 211 SEQRES 1 B 210 VAL PRO GLN SER ILE ASP TRP ARG ASP TYR GLY ALA VAL SEQRES 2 B 210 THR SER VAL LYS ASN GLN ASN PRO CYS GLY ALA CYS TRP SEQRES 3 B 210 ALA PHE ALA ALA ILE ALA THR VAL GLU SER ILE TYR LYS SEQRES 4 B 210 ILE LYS LYS GLY ILE LEU GLU PRO LEU SER GLU GLN GLN SEQRES 5 B 210 VAL LEU ASP CYS ALA LYS GLY TYR GLY CYS LYS GLY GLY SEQRES 6 B 210 TRP GLU PHE ARG ALA PHE GLU PHE ILE ILE SER ASN LYS SEQRES 7 B 210 GLY VAL ALA SER GLY ALA ILE TYR PRO TYR LYS ALA ALA SEQRES 8 B 210 LYS GLY THR CYS LYS THR ASP GLY VAL PRO ASN SER ALA SEQRES 9 B 210 TYR ILE THR GLY TYR ALA ARG VAL PRO ARG ASN ASN GLU SEQRES 10 B 210 SER SER MET MET TYR ALA VAL SER LYS GLN PRO ILE THR SEQRES 11 B 210 VAL ALA VAL ASP ALA ASN ALA ASN PHE GLN TYR TYR LYS SEQRES 12 B 210 SER GLY VAL PHE ASN GLY PRO CYS GLY THR SER LEU ASN SEQRES 13 B 210 HIS ALA VAL THR ALA ILE GLY TYR GLY GLN ASP SER ILE SEQRES 14 B 210 ILE TYR PRO LYS LYS TRP GLY ALA LYS TRP GLY GLU ALA SEQRES 15 B 210 GLY TYR ILE ARG MET ALA ARG ASP VAL SER SER SER SER SEQRES 16 B 210 GLY ILE CYS GLY ILE ALA ILE ASP PRO LEU TYR PRO THR SEQRES 17 B 210 LEU GLU MODRES 1W0Q ASN B 117 ASN GLYCOSYLATION SITE HET AGC B1213 20 HET MAN B1216 22 HET NGZ B1217 27 HET RAM B1214 21 HET NDG B1215 26 HET XYZ B1212 18 HETNAM AGC ALPHA-D-GLUCOSE HETNAM MAN ALPHA-D-MANNOSE HETNAM NGZ 2-(ACETYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSE HETNAM RAM RHAMNOSE HETNAM NDG 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE HETNAM XYZ BETA-D-XYLOFURANOSE FORMUL 2 AGC C6 H12 O6 FORMUL 2 MAN C6 H12 O6 FORMUL 2 NGZ C8 H15 N O6 FORMUL 2 RAM C6 H12 O5 FORMUL 2 NDG C8 H15 N O6 FORMUL 3 XYZ C5 H10 O5 HELIX 1 1 ALA B 25 GLY B 44 1 20 HELIX 2 2 SER B 50 ALA B 58 1 9 HELIX 3 3 TYR B 61 CYS B 63 5 3 HELIX 4 4 TRP B 67 ASN B 78 1 12 HELIX 5 5 ASN B 117 GLN B 128 1 12 HELIX 6 6 GLY B 197 ASP B 204 5 8 SHEET 1 BA 2 ILE B 6 ASP B 7 0 SHEET 2 BA 2 GLY B 164 TYR B 165 -1 O TYR B 165 N ILE B 6 SHEET 1 BB 2 GLY B 109 ARG B 112 0 SHEET 2 BB 2 LEU B 206 THR B 209 -1 O TYR B 207 N ALA B 111 SHEET 1 BC 2 ILE B 130 VAL B 134 0 SHEET 2 BC 2 HIS B 158 ALA B 162 -1 O HIS B 158 N VAL B 134 SSBOND 1 CYS B 23 CYS B 63 SSBOND 2 CYS B 57 CYS B 96 SSBOND 3 CYS B 152 CYS B 199 LINK ND2 ASN B 117 C1 NDG B1215 LINK C1 XYZ B1212 O2 AGC B1213 LINK O6 AGC B1213 C1 MAN B1216 LINK C1 AGC B1213 O4 NGZ B1217 LINK C1 RAM B1214 O3 NDG B1215 LINK O4 NDG B1215 C1 NGZ B1217 CISPEP 1 ILE B 107 THR B 108 0 7.32 CISPEP 2 GLY B 150 PRO B 151 0 0.08 SITE 1 XYZ 1 ASN B 116 SITE 1 RAM 2 ASN B 116 ASN B 117 SITE 1 NDG 4 PRO B 114 ARG B 115 ASN B 116 ASN B 117 SITE 1 NGZ 3 PRO B 114 ARG B 115 ASN B 116 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 MASTER 171 0 6 6 6 0 4 6 0 0 0 17 END