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(-) Description

Title :  CRYSTAL STRUCTURE OF PENICILLIN G ACYLASE FROM THE BRO1 MUTANT STRAIN OF PROVIDENCIA RETTGERI
 
Authors :  M. A. Mcdonough, H. E. Klei, J. A. Kelly
Date :  12 Jun 99  (Deposition) - 24 Jun 99  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Antibiotic Resistance, Amidohydrolase, Ntn-Hydrolase Fold, N-Terminal Pyroglutamate, Penicillin Binding Protein, Calcium Binding Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Mcdonough, H. E. Klei, J. A. Kelly
Crystal Structure Of Penicillin G Acylase From The Bro1 Mutant Strain Of Providencia Rettgeri.
Protein Sci. V. 8 1971 1999
PubMed-ID: 10548042

(-) Compounds

Molecule 1 - PENICILLIN G AMIDASE
    Cellular Location: PERIPLASM
    Chains: A
    Fragment: UNP RESIDUES 24-228
    Mutation: YES
    Organism Scientific: PROVIDENCIA RETTGERI
    Organism Taxid: 587
    Other Details: CHAIN A IS ALPHA-SUBUNIT
    Variant: 31052
 
Molecule 2 - PENICILLIN G AMIDASE
    Cellular Location: PERIPLASM
    Chains: B
    Fragment: UNP RESIDUES 285-837
    Organism Scientific: PROVIDENCIA RETTGERI
    Organism Taxid: 587
    Other Details: CHAIN B IS BETA-SUBUNIT
    Variant: 31052

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2PCA2Mod. Amino AcidPYROGLUTAMIC ACID
3SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:150 , ASP B:73 , VAL B:75 , ASP B:76 , PRO B:205 , ASP B:252BINDING SITE FOR RESIDUE CA B 554
2AC2SOFTWARELYS B:98 , ARG B:270 , GLN B:288 , HOH B:775BINDING SITE FOR RESIDUE SO4 B 555
3AC3SOFTWAREPCA A:1 , SER A:2 , THR A:3 , GLN A:4 , ASN A:20 , HOH A:828 , HOH A:830BINDING SITE FOR RESIDUE SO4 A 255
4AC4SOFTWARETHR A:128 , PHE A:130 , GLU B:491 , SER B:494 , HOH B:981BINDING SITE FOR RESIDUE SO4 A 269
5AC5SOFTWAREGLN B:200 , ASN B:441 , ASN B:444 , HOH B:1038BINDING SITE FOR RESIDUE SO4 B 556
6ASAUTHORSER B:1 , GLN B:23 , ALA B:69 , ASN B:241SER B 1 IS THE CATALYTIC RESIDUE GLN B 23, ALA B 69 AND ASN B 241 FORM AN OXYANION HOLE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CP9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Asn B:28 -Pro B:29
2Ala B:365 -Pro B:366
3Ala B:500 -Pro B:501

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CP9)

(-) Exons   (0, 0)

(no "Exon" information available for 1CP9)

(-) Sequences/Alignments

Asymmetric 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:197
 aligned with Q7WZI9_PRORE | Q7WZI9 from UniProtKB/TrEMBL  Length:837

    Alignment length:197
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
         Q7WZI9_PRORE    24 QSTQIKIERDNYGVPHIYANDTYSLFYGYGYAVAQDRLFQMEMAKRSTQGTVSEVFGKDYISFDKEIRNNYWPDSIHKQINQLPSQEQDILRGYADGMNAWIKQINTKPDDLMPKQFIDYDFLPSQWTSFDVAMIMVGTMANRFSDMNSEIDNLALLTALKDKYGEQLGVEFFNQINWLNNPNAPTTISSEEFTYSD 220
               SCOP domains d1cp9.1 A:,B: Penicillin acylase                                                                                                                                                                      SCOP domains
               CATH domains -1cp9A01 A:2-147 Penicillin Amidohydrolase, domain 1                                                                                               1cp9A02 A:148-177             -------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee.....eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhh.hhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhh..hhhhhh........hhhhhhhhhhh.hhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cp9 A   1 xSTQIKIERDNYGVPHIYANDTYSLFYGYGYAVAQDRLFQMEMAKRSTQGTVSEVFGKDYISFDKEIRNNYWPDSIHKQINQLPSQEQDILRGYADGMNAWIKQINTKPDDLMPKQFIDYDFLPSQWTSFDVAMIMVGTLANRFSDMNSEIDNLALLTALKDKYGEQLGVEFFNQINWLNNPNAPTTISSEEFTYSD 197
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
                            |                                                                                                                                                                                                    
                            1-PCA                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:553
 aligned with Q7WZI9_PRORE | Q7WZI9 from UniProtKB/TrEMBL  Length:837

    Alignment length:553
                                   294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834   
         Q7WZI9_PRORE   285 SNVWLVGKTKASGAKAILLNGPQFGWFNPAYTYGIGLHGAGFNIVGNTPFAYPAILFGHNGHVSWGSTAGFGDGVDIFAEQVSPEDPNSYLHQGQWKKMLSRQETLNVKGEQPITFEIYRTVHGNVVKRDKTTHTAYSKARAWDGKELTSLMAWVKQGQAQNWQQWLDQAQNQALTINWYYADKDGNIGYVHTGHYPDRQINHDPRLPVSGTGEWDWKGIQPFANNPKVYNPKSGYIANWNNSPAKNYPASDLFAFLWGSADRVKEIDNRIEAYDKLTADDMWAILQQTSRVDLNHRLFTPFLTQATQGLPSNDNSVKLVSMLQQWDGINQLSSDGKHYIHPGSAILDIWLKEMLKATLGQTVPAPFDKWYLASGYETTQEGPTGSLNISTGAKLLYESLLEDKSPISQSIDLFSGQPQNDVIRKTLNTTYQKMIEKYGDNPANWQTPATALTFRENNFFGIPQALPQENFHQNEYHNRGTENDLIVFTEEGVSAWDVVAPGQSGFISPQGKPSPHYQDQLSLYQQFGKKPLWLNSEDVAPYIESTETLIIER 837
               SCOP domains d1cp9.1 A:,B: Penicillin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1cp9B01 B:1-72,B:146-290,B:452-532                                      1cp9B02 B:73-145  [code=2.30.120.10, no name defined]                    1cp9B01 B:1-72,B:146-290,B:452-532 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                    1cp9B03 B:291-451  [code=1.10.1400.10, no name defined]                                                                                                          1cp9B01 B:1-72,B:146-290,B:452-532                                               --------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) .eeeee.........eeeeee..........eeeeeeee..-------hhh.....eee...eeeeeee.....eeeeeeeee..eeeeeee..eeee.eeeeeee.......eeeeeee....eeeeee....eeeeeee.....hhhhhhhhhhhhh...hhhhhhhhhh....eeeeeee....eeeeee.............................hhh..eee.....eeee.......................hhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhh........hhhhhhhhhh..................hhhhhhhhhhhhhhh.hhhh....hhhh....................hhhhhhhhhh.hhh..............hhhhhhhhhhhhhhhhhhhh...hhh.......eee................eee.........eeeeee....eeeeee......................hhhhh....eee...hhhhhhh........... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------eeeeeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cp9 B   1 SNVWLVGKTKASGAKAILLNGPQFGWFNPAYTYGIGLHGAGFNIVGNTPFAYPAILFGHNGHVSWGSTAGFGDGVDIFAEQVSPEDPNSYLHQGQWKKMLSRQETLNVKGEQPITFEIYRTVHGNVVKRDKTTHTAYSKARAWDGKELTSLMAWVKQGQAQNWQQWLDQAQNQALTINWYYADKDGNIGYVHTGHYPDRQINHDPRLPVSGTGEWDWKGIQPFANNPKVYNPKSGYIANWNNSPAKNYPASDLFAFLWGSADRVKEIDNRIEAYDKLTADDMWAILQQTSRVDLNHRLFTPFLTQATQGLPSNDNSVKLVSMLQQWDGINQLSSDGKHYIHPGSAILDIWLKEMLKATLGQTVPAPFDKWYLASGYETTQEGPTGSLNISTGAKLLYESLLEDKSPISQSIDLFSGQPQNDVIRKTLNTTYQKMIEKYGDNPANWQTPATALTFRENNFFGIPQALPQENFHQNEYHNRGTENDLIVFTEEGVSAWDVVAPGQSGFISPQGKPSPHYQDQLSLYQQFGKKPLWLNSEDVAPYIESTETLIIER 553
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 1)

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

(-) CATH Domains  (5, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CP9)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7WZI9_PRORE | Q7WZI9)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

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