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(-) Description

Title :  STRUCTURE OF 6-AMINOHEXANOATE CYCLIC DIMER HYDROLASE
 
Authors :  N. Shibata
Date :  26 May 09  (Deposition) - 03 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Alpha/Beta Fold, Hydrolase, Nylon Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yasuhira, N. Shibata, G. Mongami, Y. Uedo, Y. Atsumi, Y. Kawashima, A. Hibino, Y. Tanaka, Y. -H. Lee, D. Kato, M. Takeo, Y. Higuchi, S. Negor
X-Ray Crystallographic Analysis Of The 6-Aminohexanoate Cyclic Dimer Hydrolase: Catalytic Mechanism And Evolution O An Enzyme Responsible For Nylon-6 Byproduct Degradation
J. Biol. Chem. V. 285 1239 2010
PubMed-ID: 19889645  |  Reference-DOI: 10.1074/JBC.M109.041285

(-) Compounds

Molecule 1 - 6-AMINOHEXANOATE-CYCLIC-DIMER HYDROLASE
    Chains: A
    EC Number: 3.5.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTHROBACTER SP.
    Organism Taxid: 388925
    Other Details: THIS BACTERIUM HAD BEEN CALLED FLAVOBACTERIUM SP. BUT REASSIGNED TO ARTHROBACTER STRAIN
    Strain: KI72
    Synonym: NYLON OLIGOMERS-DEGRADING ENZYME EI

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:266 , GLY A:269 , PHE A:271 , GLY A:283 , ILE A:440 , HOH A:862BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A2P)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:149 -Ser A:150
2Gly A:197 -Pro A:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A2P)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMIDASESPS00571 Amidases signature.NYLA_FLASK148-179  1A:148-179
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMIDASESPS00571 Amidases signature.NYLA_FLASK148-179  1A:148-179
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMIDASESPS00571 Amidases signature.NYLA_FLASK148-179  2A:148-179

(-) Exons   (0, 0)

(no "Exon" information available for 3A2P)

(-) 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:483
 aligned with NYLA_FLASK | P13398 from UniProtKB/Swiss-Prot  Length:493

    Alignment length:483
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482   
           NYLA_FLASK     3 KVDLWQDATAQAELVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELASGPFAGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMGNQVTTEPEAWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGSVRIPASVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFCAPTASRPYAQGISENPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHDVNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRADQVTGRAFAACVDELRYYAGKVERWWEAGWDLLILPTVTRQTPEIGELMLAKGTDLEGRQSAFISGSLQMLAFTVPFNVSGQPAISLPIGMSSDGMPIGVQIVAAYGREDLLLQVAAQLEGALPWVARRPQLLN 485
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhh.......eeeee..............hhhhhhhh......hhhhhhhhhh..eeeeee..hhhhh.........................hhhhhhhhhh....eeeeee....hhhhhhhhh.eeee............hhhhhhhh..eeeeee.hhhhhhhhhhhhh...............hhhhhh.......eeee...........hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......................hhhhhhhhhhhhh..hhhhhhh..eeeeeeee.....eeeeeeee...hhhhhhhhhhhhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------AMIDASES  PDB: A:148-179        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a2p A   3 KVDLWQDATAQAELVRSGEISRTELLEATIAHVQAVNPEINAVIIPLFEKARRESELASGPFAGVPYLLKDLTVVSQGDINTSSIKGMKESGYRADHDAYFVQRMRAAGFVLLGKTNTPEMGNQVTTEPEAWGATRNPWNLGRSVGGSSGGSGAAVAAALSPVAHGNDAAGSVRIPASVCGVVGLKPTRGRISPGPLVTDSDNVAGAAHEGLFARSVRDIAALLDVVSGHRPGDTFCAPTASRPYAQGISENPGSLRVGVLTHNPVGDFALDPECAAAARGAAAALAALGHDVNDAYPEALGDRSFLKDYSTICDVAIAREIERNGELIGRPLTEDDVEWTSWEMVKRADQVTGRAFAACVDELRYYAGKVERWWEAGWDLLILPTVTRQTPEIGELMLAKGTDLEGRQSAFISGSLQMLAFTVPFNVSGQPAISLPIGMSSDGMPIGVQIVAAYGREDLLLQVAAQLEGALPWVARRPQLLN 485
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482
   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 3A2P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A2P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A2P)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (NYLA_FLASK | P13398)
molecular function
    GO:0019874    6-aminohexanoate-cyclic-dimer hydrolase activity    Catalysis of the reaction: 1,8-diazacyclotetradecane-2,9-dione + H(2)O = N-(6-aminohexanoyl)-6-aminohexanoate.
    GO:0016884    carbon-nitrogen ligase activity, with glutamine as amido-N-donor    Catalysis of the transfer of the amide nitrogen of glutamine to a variety of substrates. GATases catalyze two separate reactions at two active sites, which are located either on a single polypeptide chain or on different subunits. In the glutaminase reaction, glutamine is hydrolyzed to glutamate and ammonia, which is added to an acceptor substrate in the synthase reaction.
    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.
biological process
    GO:0019876    nylon catabolic process    The chemical reactions and pathways resulting in the breakdown of nylon, a polymer where the main polymer chain comprises recurring amide groups; these compounds are generally formed from combinations of diamines, diacids and amino acids.

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  3a2p
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  3.5.2.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        NYLA_FLASK | P13398: 3a2q

(-) Related Entries Specified in the PDB File

3a2q THE SAME PROTEIN COMPLEXED WITH SUBSTRATE