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(-) Description

Title :  CRYSTAL STRUCTURES OF GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE: MUTATIONAL STUDY OF ACTIVATION MECHANISM
 
Authors :  J. K. Kim, I. S. Yang, H. J. Shin, K. J. Cho, E. K. Ryu, S. H. Kim, S. S. Park, K
Date :  21 Jul 05  (Deposition) - 24 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Autoproteolysis, Precursor Activation, Intermediate Structure, Cephalosporin Acylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Kim, I. S. Yang, H. J. Shin, K. J. Cho, E. K. Ryu, S. H. Kim, S. S. Park, K. H. Kim
Insight Into Autoproteolytic Activation From The Structure Of Cephalosporin Acylase: A Protein With Two Proteolytic Chemistries.
Proc. Natl. Acad. Sci. Usa V. 103 1732 2006
PubMed-ID: 16446446  |  Reference-DOI: 10.1073/PNAS.0507862103

(-) Compounds

Molecule 1 - GLUTARYL 7- AMINOCEPHALOSPORANIC ACID ACYLASE
    Chains: A
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ALPHA DOMAIN
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 405038
    Strain: GK16
 
Molecule 2 - GLUTARYL 7- AMINOCEPHALOSPORANIC ACID ACYLASE
    Chains: B
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA1 DOMAIN
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 405038
    Strain: GK16
 
Molecule 3 - GLUTARYL 7- AMINOCEPHALOSPORANIC ACID ACYLASE
    Chains: C
    EC Number: 3.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BETA2 DOMAIN
    Mutation: YES
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 405038
    Strain: GK16

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ADV)

(-) Sites  (0, 0)

(no "Site" information available for 2ADV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:130 -Pro A:131
2Trp C:252 -Pro C:253
3Thr C:378 -Pro C:379
4Thr C:465 -Pro C:466

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ADV)

(-) 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:161
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:161
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
           G7AC_PSEU7    35 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLA 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2advA00 A:6-166 Penicillin Amidohydrolase, domain 1                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2adv A   6 PQAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLA 166
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165 


Chain B from PDB  Type:PROTEIN  Length:28
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:28
                                   208       218        
           G7AC_PSEU7   199 SNSWAVAPGKTANGNALLLQNPHLSWTT 226
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh.....eeeee.eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 2adv B   1 SNSWAVAPGKTANGNALLLQNPHLSWTT  28
                                    10        20        


Chain C from PDB  Type:PROTEIN  Length:494
 aligned with G7AC_PSEU7 | P07662 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:494
                                   236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716    
           G7AC_PSEU7   227 DYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERPQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 720
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2advC03 C:270-454  [code=1.10.1400.10, no name defined]                                                                                                                                  -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee..eeeeeeeeee.....eeeeeeeeee.....eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhheee..hhhhh.....hhhhh.eee.....eeee..............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhhh.eeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2adv C  29 DYFTLYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNFKP 522
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       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
   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  (0, 0)

(no "SCOP Domain" information available for 2ADV)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ADV)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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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  Cis Peptide Bonds
    Leu A:130 - Pro A:131   [ RasMol ]  
    Thr C:378 - Pro C:379   [ RasMol ]  
    Thr C:465 - Pro C:466   [ RasMol ]  
    Trp C:252 - Pro C:253   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        G7AC_PSEU7 | P07662: 1gk0 1gk1 1or0 2ae3 2ae4 2ae5 3s8r

(-) Related Entries Specified in the PDB File

2ae3 THE SAME PROTEIN, ALPHA AND BETA(R57K) DOMAINS
2ae4 THE SAME PROTEIN, ALPHA(E159Q) AND BETA DOMAINS
2ae5 THE SAME PROTEIN, ALPHA AND BETA(S1C) DOMAINS