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(-) Description

Title :  CRYSTAL STRUCTURES OF GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE: INSIGHT INTO AUTOPROTEOLYTIC ACTIVATION
 
Authors :  J. K. Kim, I. S. Yang, S. S. Park, K. H. Kim
Date :  30 May 11  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Motif, Acylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. K. Kim, I. S. Yang, S. Rhee, Z. Dauter, Y. S. Lee, S. S. Park, K. H. Kim
Crystal Structures Of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight Into Autoproteolytic Activation.
Biochemistry V. 42 4084 2003
PubMed-ID: 12680762  |  Reference-DOI: 10.1021/BI027181X

(-) Compounds

Molecule 1 - GLUTARYL-7-AMINOCEPHALOSPORANIC-ACID ACYLASE
    ChainsA, B
    EC Number3.5.1.93
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23A
    Expression System StrainDE3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificPSEUDOMONAS
    Organism Taxid269086
    StrainSY-77-1
    SynonymGLUTARYL-7-ACA ACYLASE, 7-BETA-(4-CARBOXYBUTANAMIDO) CEPHALOSPORANIC ACID ACYLASE, GL-7-ACA ACYLASE, GCA, GLUTARYL-7- AMINOCEPHALOSPORANIC-ACID ACYLASE SUBUNIT ALPHA, GLUTARYL-7-ACA ACYLASE SUBUNIT ALPHA, GLUTARYL-7-AMINOCEPHALOSPORANIC-ACID ACYLASE SUBUNIT BETA, GLUTARYL-7-ACA ACYLASE SUBUNIT BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:76 , LEU A:148 , PRO A:153 , ASP A:164 , TYR A:199 , HOH A:813 , HOH A:893 , HOH A:1021BINDING SITE FOR RESIDUE GOL A 698
2AC2SOFTWARETHR B:76 , ARG B:143 , LEU B:148 , TYR B:199 , HOH B:746 , HOH B:938BINDING SITE FOR RESIDUE GOL B 698

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S8R)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:130 -Pro A:131
2Trp A:421 -Pro A:422
3Thr A:547 -Pro A:548
4Thr A:634 -Pro A:635
5Leu B:130 -Pro B:131
6Trp B:421 -Pro B:422
7Thr B:547 -Pro B:548
8Thr B:634 -Pro B:635

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3S8R)

(-) Exons   (0, 0)

(no "Exon" information available for 3S8R)

(-) 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:684
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:684
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       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    
           G7AC_PSEU7    35 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGSNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 718
               SCOP domains d3s8ra_ A: Cephalosporin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhh....hhhhhh.eeeeeee.hhhh.....eeeeeeeee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee.....eeeeeee.....eeeeeee........eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eeee..............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........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
                 3s8r A   6 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGANSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 689
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685    

Chain B from PDB  Type:PROTEIN  Length:686
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:686
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       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      
           G7AC_PSEU7    35 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGSNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 720
               SCOP domains d3s8rb_ B: Cephalosporin acylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------Penicil_amidase-3s8rB01 B:155-683                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------Penicil_amidase-3s8rB02 B:155-683                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------Penicil_amidase-3s8rB03 B:155-683                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------Penicil_amidase-3s8rB04 B:155-683                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                -------- Pfam domains (4)
         Sec.struct. author .............eeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhh....hhhhhh.eeeeeee.hhhh.....eeeeeeeee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee.eee..eeee..eee.....eeeeeee.....eeeeeee........eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhh.ee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8r B   6 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGANSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 691
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 1OQZ: 4,8)

(no "CATH Domain" information available for 3S8R, only for superseded entry 1OQZ replaced by 3S8R)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (G7AC_PSEU7 | P07662)
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_PSEU7 | P076621gk0 1gk1 1or0 2adv 2ae3 2ae4 2ae5

(-) Related Entries Specified in the PDB File

1or0 NATIVE PROTEIN