HEADER FIBER-FORMING PROTEIN 30-JUN-99 1QT2 TITLE BUNDLE FORMING PILIN OF ENTEROPATHOGENIC E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FIBER-FORMING PROTEIN PILIN); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FIMBRIAE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROPATHOGENIC ESCHERICHIA COLI KEYWDS TYPE 4B PILIN, FIBER FORMING PROTEIN, BUNDLE FORMING PILIN, KEYWDS 2 ENTEROPATHOGENIC ESCHERICHIA COLI, ADHESION EXPDTA THEORETICAL MODEL AUTHOR R.CHATTOPADHYAYA,A.C.GHOSE REVDAT 2 01-APR-03 1QT2 1 JRNL REVDAT 1 12-JUL-99 1QT2 0 JRNL AUTH R.CHATTOPADHYAYA,A.C.GHOSE JRNL TITL MODEL OF VIBRIO CHOLERAE TOXIN COREGULATED PILIN JRNL TITL 2 CAPABLE OF FILAMENT FORMATION JRNL REF PROTEIN ENG. V. 15 297 2002 JRNL REFN ASTM PRENE9 UK ISSN 0269-2139 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.GIRON,A.S.Y.HO,G.K.SCHOOLNIK REMARK 1 TITL AN INDUCIBLE BUNDLE FORMING PILUS OF PATHOGENIC REMARK 1 TITL 2 ESCHERICHIA COLI REMARK 1 REF SCIENCE V. 254 710 1991 REMARK 1 REFN ASTM SCIEAS US ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.S.STROM,S.LORY REMARK 1 TITL STRUCTURE-FUNCTION AND BIOGENESIS OF TYPE IV PILI REMARK 1 REF ANNU.REV.MICROBIOL. V. 47 565 1993 REMARK 1 REFN US ISSN 0066-4227 REMARK 1 REFERENCE 3 REMARK 1 AUTH H.E.PARGE,K.T.FOREST,M.J.HICKEY,D.A.CHRISTENSEN, REMARK 1 AUTH 2 E.D.GETZOFF,J.A.TAINER REMARK 1 TITL STRUCTURE OF THE FIBRE-FORMING PROTEIN PILIN AT REMARK 1 TITL 2 2.6A RESOLUTION REMARK 1 REF NATURE V. 378 32 1995 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.S.DONNENBERG,J.A.GIRON,J.P.NATARO,J.B.KAPER REMARK 1 TITL A PLASMID-ENCODED TYPE IV FIMBRIAL GENE OF REMARK 1 TITL 2 ENTEROPATHOGENIC ESCHERICHIA COLI ASSOCIATED WITH REMARK 1 TITL 3 LOCALIZED ADHERENCE REMARK 1 REF MOL.MICROBIOL. V. 6 3427 1992 REMARK 1 REFN ASTM MOMIEE UK ISSN 0950-382X REMARK 1 REFERENCE 5 REMARK 1 AUTH I.SOHEL,J.L.PUENTE,W.J.MURRAY,J.VUOPIO-VARKILA, REMARK 1 AUTH 2 G.K.SCHOOLNIK REMARK 1 TITL CLONING AND CHARACTERIZATION OF THE BUNDLE-FORMING REMARK 1 TITL 2 PILIN GENE OF ENTEROPATHOGENIC ESCHERICHIA COLI REMARK 1 REF MOL.MICROBIOL. V. 7 563 1993 REMARK 1 REFN ASTM MOMIEE UK ISSN 0950-382X 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 1QT2 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 6 REMARK 6 ENTEROPATHOGENIC ESCHERICHIA COLI IS A CAUSE OF REMARK 6 CHILDHOOD DIARRHEA. IT GROWS ON THE SURFACE OF THE REMARK 6 SMALL INTESTINE AND ON CULTURED EPITHELIAL CELLS AS REMARK 6 COLONIES OF ADHERENT BACTERIA (REF. 1). THIS REMARK 6 BACTERIUM EXPRESSES ROPELIKE BUNDLES OF FILAMENTS REMARK 6 UNDER SOME CONDITIONS, CREATING A NETWORK OF FIBRES REMARK 6 THAT BIND TOGETHER INDIVIDUAL BACTERIA WITH OTHERS. REMARK 6 THESE FIBRES ARE CALLED BUNDLE-FORMING PILI (BFP). REMARK 6 THUS BFP IS THOUGHT TO BE AN CRITICAL FACTOR IN REMARK 6 FORMATION OF COLONIES ESSENTIAL FOR THE PROPAGATION REMARK 6 OF THE DISEASE. ELECTRON MICROSCOPY SHOWED THAT REMARK 6 WHEN A STRAIN OF THE ENTEROPATHOGENIC E. COLI WAS REMARK 6 GROWN ON COLONIZATION FACTOR AGAR, 10 TO 30 FILAMENTS REMARK 6 WERE NOTICED PROJECTING FROM EACH BACTERIUM, HAVING REMARK 6 A DIAMETER OF 70 ANGSTROMS EACH. WHEN THE SAME STRAIN REMARK 6 WAS GROWN ON A DIFFERENT MEDIA CONTAINING SHEEP BLOOD, REMARK 6 LONG, ROPE LIKE STRUCTURES OF 500 TO 5000 ANGSTROM REMARK 6 DIAMETER WERE FORMED (REF. 1). REMARK 6 REMARK 6 THE 180 AA PROTEIN BFPA IS THE MAJOR COMPONENT OF THESE REMARK 6 PILI AND HAS A MOLECULAR WEIGHT OF 19.5 KILODALTONS. REMARK 6 REMARK 6 BFPA IS A MEMBER OF THE TYPE-IV PILI INVOLVED IN REMARK 6 ADHESION TO HOST CELL SURFACES. MANY OTHER BACTERIA REMARK 6 POSSESS SIMILAR PILI (REF.2 ABOVE). BFPA IS CLASSIFIED REMARK 6 WITHIN THE SUBTYPE IVB, INDICATING THAT IT HAS HIGHER REMARK 6 SIMILARITY WITH THE TOXIN COREGULATED PILUS OF VIBRIO REMARK 6 CHOLERAE (TCPA) AND LONGUS OF ENTEROTOXIGENIC E.COLI. REMARK 6 THE TYPE IV PILI ARE 1,000-4,000 NM LONG, 60-90 ANGS- REMARK 6 TROM DIAMETER FIBRES FORMED BY ORDERED ASSOCIATION REMARK 6 OF THOUSANDS OF IDENTICAL PILIN SUBUNITS PLUS A FEW REMARK 6 COPIES OF PILUS ASSOCIATED PROTEINS. REMARK 6 REMARK 6 THE CRYSTAL STRUCTURE OF THE 158 RESIDUE NEISSERIA REMARK 6 GONORRHOEAE PILIN SHOWED AN ELONGATED LADLE SHAPED REMARK 6 PILIN STRUCTURE (REF. 3 ABOVE AND PDB ENTRY 1AY2). REMARK 6 REMARK 6 WE PREVIOUSLY CONSTRUCTED A THREE DIMENSIONAL MODEL REMARK 6 OF THE VIBRIO CHOLERAE PILIN (TCPA) COMBINING REMARK 6 BIOCHEMICAL DATA IN THE LITERATURE SO FAR ABOUT TCPA REMARK 6 WITH PROTEIN STRUCTURAL PRINCIPLES AND THE CRYSTAL REMARK 6 STRUCTURE OF THE NEISSERIA GONORRHOEAE PILIN (1AY2). REMARK 6 OUR TCPA MODEL HAS PDB CODE 1QQZ. THIS MODEL OF REMARK 6 TCPA SATISFIES THE BIOCHEMICAL DATA. SIMILAR DATA REMARK 6 IS NOT AVAILABLE IN THE LITERATURE FOR BFPA. REMARK 6 SINCE AN UNDERSTANDING OF THE THREE DIMENSIONAL REMARK 6 STRUCTURE OF BFPA IS EXPECTED TO BE OF CONSIDERABLE REMARK 6 INTEREST, WE MODELLED THE BFPA STRUCTURE USING REMARK 6 SIMILAR APPROACHES USED FOR BUILDING THE TCPA REMARK 6 MODEL. BOTH V. CHOLERAE AND EPEC ARE ENTEROPATHO REMARK 6 -GENIC ORGANISMS AND THEIR PILINS SHOULD HAVE REMARK 6 SIMILAR THREE DIMENSIONAL STRUCTURES. REMARK 6 REMARK 6 PROTECTION AGAINST VIBRIO CHOLERAE WAS ACHIEVED REMARK 6 BY RAISING ANTIBODIES AGAINST SEVERAL PEPTIDES REMARK 6 ON THE FIBRE SURFACE OF TCPA AND USING THESE REMARK 6 ANTIBODIES TO PROTECT INFANT MICE INFECTED BY VIBRIO REMARK 6 CHOLERAE. SIMILARLY, FROM OUR MODEL PROPOSED REMARK 6 HERE, IT WILL BE POSSIBLE TO DESIGN PEPTIDES ON REMARK 6 THE OUTER SURFACE OF THE FIBRE FOR THE PURPOSE REMARK 6 OF RAISING ANTIBODIES AGAINST ENTEROPATHOGENIC REMARK 6 E. COLI THAT COULD PREDICTABLY BE PROTECTIVE. REMARK 6 REMARK 6 THE BFPA MOLECULE IN OUR MODEL HAS AN ELONGATED REMARK 6 (85 X 38 X 24A) LADLE SHAPED PILIN STRUCTURE, SIMILAR REMARK 6 TO THE N. GONORRHOEAE PILIN (PILE), THE SIZE OF THE REMARK 6 GLOBULAR DOMAIN BEING LARGER IN THE 180 RESIDUE BFP. REMARK 6 THE PILE CRYSTAL STRUCTURE (REF.3 AND PDB CODE 1AY2) REMARK 6 HAS BEEN USED BY US TO BUILD THE BFP MODEL UP TO REMARK 6 RESIDUE 139. AFTER THIS RESIDUE, BFP AND PILE REMARK 6 POSSESS DIFFERENT FOLDS, HOWEVER BFP POSSESSES A REMARK 6 TOPOLOGY LIKE TCPA BETWEEN RESIDUES 140-180. REMARK 6 REMARK 6 THERE IS ONE PILIN MOLECULE IN THIS ENTRY. IN THE REMARK 6 FIBER, EACH MOLECULE WILL BE RELATED TO ITS ADJACENT REMARK 6 MOLECULE BY A 72 DEGREE ROTATION ABOUT THE FIBER REMARK 6 AXIS AND A 8.2 ANGSTROM TRANSLATION PARALLEL TO THE REMARK 6 FIBRE AXIS. SIX MOLECULES ARE INCLUDED IN THE PDB ENTRY REMARK 6 1QQZ INDICATING FIBER FORMATION FOR TCPA. FIBER REMARK 6 FORMATION FOR BFP MUST BE VERY SIMILAR, THOUGH NOT REMARK 6 INDICATED IN THIS ENTRY. THE DIAMETER OF THE REMARK 6 PENTAMERIC BFPA FILAMENT IS EXPECTED TO BE SMALLER REMARK 6 THAN THAT FOR TCPA (81A) BUT LARGER THAN THAT FOR REMARK 6 PILE (70A). REMARK 7 REMARK 7 MODEL BUILDING FOR THE BUNDLE-FORMING PILIN WAS REMARK 7 CARRIED OUT USING THE INSIGHT-II PACKAGE INCLUDING REMARK 7 PROGRAMS DISCOVER AND HOMOLOGY REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-1999. REMARK 100 THE RCSB ID CODE IS RCSB001205. 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 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 LEU A 60 141.49 71.69 REMARK 500 ILE A 83 -58.98 66.14 REMARK 500 THR A 100 -35.17 78.94 REMARK 500 ASP A 112 -107.24 79.85 REMARK 500 ILE A 135 -45.35 70.41 REMARK 500 ALA A 148 -50.73 68.16 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 THR A 84 ASN A 85 -142.83 DBREF 1QT2 A 1 180 UNP P33553 BFPA_ECOLI 14 193 SEQRES 1 A 180 LEU SER LEU ILE GLU SER ALA MET VAL LEU ALA LEU ALA SEQRES 2 A 180 ALA THR VAL THR ALA GLY VAL MET PHE TYR TYR GLN SER SEQRES 3 A 180 ALA SER ASP GLY ASN LYS SER GLN ASN ALA ILE SER GLU SEQRES 4 A 180 VAL MET SER ALA THR SER ALA ILE ASN GLY LEU TYR ILE SEQRES 5 A 180 GLY GLN THR SER TYR SER GLY LEU ASP SER THR ILE LEU SEQRES 6 A 180 LEU ASN THR SER ALA ILE PRO ASP ASN TYR LYS ASP THR SEQRES 7 A 180 THR ASN LYS LYS ILE THR ASN PRO PHE GLY GLY GLU LEU SEQRES 8 A 180 ASN VAL GLY PRO ALA ASN ASN ASN THR ALA PHE GLY TYR SEQRES 9 A 180 TYR LEU THR LEU THR ARG LEU ASP LYS ALA ALA CYS VAL SEQRES 10 A 180 SER LEU ALA THR LEU ASN LEU GLY THR SER ALA LYS GLY SEQRES 11 A 180 TYR GLY VAL ASN ILE SER GLY GLU ASN ASN ILE THR SER SEQRES 12 A 180 PHE GLY ASN SER ALA ASP GLN ALA ALA LYS SER THR ALA SEQRES 13 A 180 ILE THR PRO ALA GLU ALA ALA THR ALA CYS LYS ASN THR SEQRES 14 A 180 ASP SER THR ASN LYS VAL THR TYR PHE MET LYS HELIX 1 1 SER A 2 ALA A 43 1 42 HELIX 2 2 ALA A 43 GLY A 53 1 11 HELIX 3 3 ASP A 149 ALA A 162 1 14 SHEET 1 A 3 ASN A 85 GLY A 88 0 SHEET 2 A 3 PHE A 102 THR A 109 -1 O GLY A 103 N PHE A 87 SHEET 3 A 3 LYS A 113 SER A 118 -1 N ALA A 114 O LEU A 108 SHEET 1 B 2 THR A 121 GLY A 125 0 SHEET 2 B 2 ALA A 128 TYR A 131 -1 O ALA A 128 N GLY A 125 SSBOND 1 CYS A 116 CYS A 166 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 174 0 0 3 5 0 0 6 0 0 0 14 END