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(-) Description

Title :  OXIDIZED PENICILLIN V ACYLASE FROM B. SPHAERICUS
 
Authors :  C. G. Suresh, A. V. Pundle, K. N. Rao, H. Sivaraman, J. A. Brannigan, C. E. Mcvey, C. S. Verma, Z. Dauter, E. J. Dodson, G. G. Dodson
Date :  13 Nov 98  (Deposition) - 26 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Amidohydrolase, Ntn Hydrolase, Penicillin V Acylase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. G. Suresh, A. V. Pundle, H. Sivaraman, K. N. Rao, J. A. Brannigan, C. E. Mcvey, C. S. Verma, Z. Dauter, E. J. Dodson, G. G. Dodson
Penicillin V Acylase Crystal Structure Reveals New Ntn-Hydrolase Family Members.
Nat. Struct. Biol. V. 6 414 1999
PubMed-ID: 10331865  |  Reference-DOI: 10.1038/8213
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLIN V ACYLASE
    Chains: A, B, C, D
    Collection: NCIM 2478
    EC Number: 3.5.1.11
    Organism Scientific: LYSINIBACILLUS SPHAERICUS
    Organism Taxid: 1421
    Synonym: PENICILLIN V AMIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DTD4Ligand/IonDITHIANE DIOL
2OCS4Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:19 , PHE A:21 , TYR A:82BINDING SITE FOR RESIDUE DTD A 1001
2AC2SOFTWAREOCS B:1 , PHE B:21 , MET B:80 , TYR B:82 , HOH B:1183BINDING SITE FOR RESIDUE DTD B 1002
3AC3SOFTWAREPHE C:21 , TYR C:82BINDING SITE FOR RESIDUE DTD C 1003
4AC4SOFTWAREPHE D:21 , TYR D:82 , LEU D:142BINDING SITE FOR RESIDUE DTD D 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PVA)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:176 -Pro A:177
2Ser B:176 -Pro B:177
3Ser C:176 -Pro C:177
4Ser D:176 -Pro D:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PVA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PVA)

(-) Exons   (0, 0)

(no "Exon" information available for 2PVA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:332
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 335
               SCOP domains d2pvaa_ A: Penicillin V acylase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2pvaA00 A:2-332 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeeee......eeeee.....ee.......ee.....eeeeee......ee.eeee....eeeeee...............eeehhhhhhhhhhhhh.hhhhhhhhhh.eee.............eeeeee.....eeeeeee..eeeeee....ee....hhhhhhhhhhhhh.........eee..eee.....hhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..............eeeeeeeee....eeeeee..eeeeeeee.hhh.......eeee.......ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pva A   1 cSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 332
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
                            |                                                                                                                                                                                                                                                                                                                                           
                            1-OCS                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:332
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 335
               SCOP domains d2pvab_ B: Penicillin V acylase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2pvaB00 B:2-332 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeeee......eeeee.....ee.......ee.....eeeeee......ee.eeee....eeeeee...............eeehhhhhhhhhhhhh.hhhhhhhhhhheee.............eeeeee.....eeeeeee..eeeee.....ee....hhhhhhhhhhhhh.........eee..eee.....hhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..............eeeeeeeee....eeeeee..eeeeeeee...........eee........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pva B   1 cSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 332
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
                            1-OCS                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:332
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 335
               SCOP domains d2pvac_ C: Penicillin V acylase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2pvaC00 C:2-332 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeeeeee......eeeee.....ee.......ee.....eeeeee......ee.eeee....eeeeee...............eee...hhhhhhhhhh.hhhhhhhhhh.eee.............eeeeee.....eeeeeee..eeeee.....ee....hhhhhhhhhhhhh.........eee..eee.....hhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh................eeeeeeeee....eeeeee..eeeeeeee...........eee........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pva C   1 cSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 332
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
                            1-OCS                                                                                                                                                                                                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:332
 aligned with PAC_LYSSH | P12256 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:332
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
            PAC_LYSSH     4 CSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 335
               SCOP domains d2pvad_ D: Penicillin V acylase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -2pvaD00 D:2-332 Penicillin V Acylase; Chain A                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) CBAH-2pvaD01 D:1-317                                                                                                                                                                                                                                                                                                         --------------- Pfam domains (1)
           Pfam domains (2) CBAH-2pvaD02 D:1-317                                                                                                                                                                                                                                                                                                         --------------- Pfam domains (2)
           Pfam domains (3) CBAH-2pvaD03 D:1-317                                                                                                                                                                                                                                                                                                         --------------- Pfam domains (3)
           Pfam domains (4) CBAH-2pvaD04 D:1-317                                                                                                                                                                                                                                                                                                         --------------- Pfam domains (4)
         Sec.struct. author ..eeeee.....eeeeeeeee......eeeee.....ee.......ee.....eeeeee......ee.eeee....eeeeee...............eeehhhhhhhhhhhhh.hhhhhhhhhhheee.............eeeeee.....eeeeeee..eeeee.....ee....hhhhhhhhhhhhh.........eee..eee.....hhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh................eeeeeeeee....eeeeee..eeeeeeee...........eee........ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pva D   1 cSSLSIRTTDDKSLFARTMDFTMEPDSKVIIVPRNYGIRLLEKENVVINNSYAFVGMGSTDITSPVLYDGVNEKGLMGAMLYYATFATYADEPKKGTTGINPVYVISQVLGNCVTVDDVIEKLTSYTLLNEANIILGFAPPLHYTFTDASGESIVIEPDKTGITIHRKTIGVMTNSPGYEWHQTNLRAYIGVTPNPPQDIMMGDLDLTPFGQGAGGLGLPGDFTPSARFLRVAYWKKYTEKAKNETEGVTNLFHILSSVNIPKGVVLTNEGKTDYTIYTSAMCAQSKNYYFKLYDNSRISAVSLMAENLNSQDLITFEWDRKQDIKQLNQVN 332
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330  
                            1-OCS
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PAC_LYSSH | P12256)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0008953    penicillin amidase activity    Catalysis of the reaction: penicillin + H2O = a carboxylate + 6-aminopenicillanate.
biological process
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PAC_LYSSH | P12256: 2iwm 2quy 2z71 3mji 3pva

(-) Related Entries Specified in the PDB File

3pva