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(-) Description

Title :  STRUCTURE OF CEPHALOSPORIN ACYLASE IN COMPLEX WITH GLUTARYL-7-AMINOCEPHALOSPORANIC ACID
 
Authors :  Y. Kim, W. G. J. Hol
Date :  01 Sep 01  (Deposition) - 01 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cephalosporin Acylase, Glutaryl-7-Aminocephalosporanic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, W. G. Hol
Structure Of Cephalosporin Acylase In Complex With Glutaryl-7-Aminocephalosporanic Acid And Glutarate: Insight Into The Basis Of Its Substrate Specificity
Chem. Biol. V. 8 1253 2001
PubMed-ID: 11755403  |  Reference-DOI: 10.1016/S1074-5521(01)00092-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CEPHALOSPORIN ACYLASE ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 30-187
    Organism Scientific: BREVUNDIMONAS DIMINUTA
    Organism Taxid: 293
    Synonym: GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE
 
Molecule 2 - CEPHALOSPORIN ACYLASE BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24D(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 199-718
    Organism Scientific: BREVUNDIMONAS DIMINUTA
    Organism Taxid: 293
    Synonym: GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1CEN1Ligand/Ion7BETA-(4CARBOXYBUTANAMIDO) CEPHALOSPORANIC ACID
2MSE13Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:148 , TYR A:149 , SER A:152 , ARG A:155 , SER B:170 , HIS B:192 , LEU B:193 , TYR B:202 , GLN B:219 , ARG B:226 , PHE B:227 , VAL B:239 , HOH B:1304 , HOH B:1305BINDING SITE FOR RESIDUE CEN B 999

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:130 -Pro A:131
2Trp B:421 -Pro B:422
3Thr B:547 -Pro B:548
4Thr B:634 -Pro B:635

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JVZ)

(-) 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:152
 aligned with G7AC_BREDI | Q9L5D6 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:152
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  
           G7AC_BREDI    36 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLG 187
               SCOP domains d1jvz.1 A:,B: Cephalosporin acylase                                                                                                                      SCOP domains
               CATH domains 1jvzA00 A:7-158 Penicillin Amidohydrolase, domain 1                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvz A   7 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLmNFLYVASPGRTLG 158
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156  
                                                                                                                                                                    145-MSE         


Chain B from PDB  Type:PROTEIN  Length:520
 aligned with G7AC_BREDI | Q9L5D6 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:520
                                   208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718
           G7AC_BREDI   199 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGSTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITAHSFDDYEAAMARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGNVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPRDHPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQFSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAAFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGIRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 718
               SCOP domains d1jvz.1 A:,B: Cephalosporin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jvzB01 B:170-244,B:311-436,B:620-677                                      1jvzB03 B:245-310  [code=2.30.120.10, no name defined]            1jvzB01 B:170-244,B:311-436,B:620-677 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                              --1jvzB02 B:439-619  [code=1.10.1400.10, no name defined]                                                                                                                              1jvzB01 B:170-244,B:311-436,B:620-677                     ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh.....eeeee.eee..hhhh.eeeeeeee..eeeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee..eeeeeeeeee.....eeeeeeeeee.....eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..........hhhhhhhhhhhhhh........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvz B 170 SNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRmGITNTVNGmVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGSTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGmLEQYFDmITAHSFDDYEAAmARmQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGNVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYCPANHPSYLAPQTPHSLRAQQSVRLmSENDDLTLERFmALQFSHRAVmADRTLPDLIPAALIDPDPEVQAAARLLAAWDRDFTSDSRAALLFEEWARLFAGQNFAGQAAFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRmILNDVNVPGAAGYGNLGSFRVFTWSDPDENGIRTPVHGETWVAmIEFSTPVRAYGLmSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 689
                                   179       189       199       209       219       229   |   239  |    249       259       269       279       289       299       309       319     | 329       339 |     349       359       369       379       389       399       409       419       429       439       449 |     459   |   469   |   479       489       499       509       519       529       539       549       559       569       579     | 589       599       609       619       629       639  |    649       659       669       679       689
                                                                                         233-MSE  242-MSE                                                                     318-MSE  |          338-MSE                                                                                                          451-MSE     463-MSE   473-MSE                                                                                                         585-MSE                                     629-MSE      642-MSE                                           
                                                                                                                                                                                     325-MSE         341-MSE
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G7AC_BREDI | Q9L5D6)
molecular function
    GO:0033968    glutaryl-7-aminocephalosporanic-acid acylase activity    Catalysis of the reaction: (7R)-7-(4-carboxybutanamido)cephalosporanate + H2O = (7R)-7-aminocephalosporanate + glutarate.
    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.
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.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        G7AC_BREDI | Q9L5D6: 1fm2 1jw0 1keh

(-) Related Entries Specified in the PDB File

1jw0 1JW0 CONTAINS THE SAME PROTEIN WITH GLUTARATE.