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(-) Description

Title :  THE FUNCTIONAL ROLE OF THE BINUCLEAR METAL CENTER IN D-AMINOACYLASE. ONE-METAL ACTIVATION AND SECOND-METAL ATTENUATION
 
Authors :  W. L. Lai, L. Y. Chou, C. Y. Ting, Y. C. Tsai, S. H. Liaw
Date :  20 Nov 03  (Deposition) - 20 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Beta Barrel, Insertion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. L. Lai, L. Y. Chou, C. Y. Ting, R. Kirby, Y. C. Tsai, A. H. Wang, S. H. Liaw
The Functional Role Of The Binuclear Metal Center In D-Aminoacylase: One-Metal Activation And Second-Metal Attenuation.
J. Biol. Chem. V. 279 13962 2004
PubMed-ID: 14736882  |  Reference-DOI: 10.1074/JBC.M308849200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-AMINOACYLASE
    Chains: A
    EC Number: 3.5.1.81
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DA1
    Mutation: YES
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:250 , LYS A:252 , TYR A:283 , GLY A:288 , SER A:289 , ASP A:366 , ARG A:377BINDING SITE FOR RESIDUE ACT A 601
2AC2SOFTWAREHIS A:67 , HIS A:69 , CYS A:96 , ASP A:366BINDING SITE FOR RESIDUE ZN A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V4Y)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:101 -Pro A:102
2Ala A:110 -Pro A:111
3Gln A:338 -Pro A:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4Y)

(-) 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:474
 aligned with Q9AGH8_ALCFA | Q9AGH8 from UniProtKB/TrEMBL  Length:484

    Alignment length:474
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477    
         Q9AGH8_ALCFA     8 PFDYILSGGTVIDGTNAPGRLADVGVRGDRIAAVGDLSASSARRRIDVAGKVVSPGFIDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGISLAPLAHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNAACMVGHSTLRAAVMPDLRREATADEIQAMQALADDALASGAIGISTGAFYPPAAHASTEEIIEVCRPLITHGGVYATHMRDEGEHIVQALEETFRIGRELDVPVVISHHKVMGKLNFGRSKETLALIEAAMASQDVSLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDVVPELQPAGAIYFMMDEPDVQRILAFGPTMIGSDGLPHDERPHPRLWGTFPRVLGHYSRDLGLFPLETAVWKMTGLTAAKFGLAERGQVQPGYYADLVVFDPATVADSATFEHPTERAAGIHSVYVNGAAVWEDQSFTGQHAGRVLNR 481
               SCOP domains d1v4ya1 A:7-61 N-acyl-D-aminoacid amidohydrolase       d1v4ya3 A:62-419 N-acyl-D-aminoacid amidohydrolase, catalytic domain                                                                                                                                                                                                                                                                                                  d1v4ya2 A:420-480 N-acyl-D-aminoacid amidohydrolase           SCOP domains
               CATH domains 1v4yA01 A:7-60,A:420-433,A:452-470                    1v4yA02 A:61-287,A:345-414 Metal-dependent hydrolases                                                                                                                                                                              1v4yA03 A:288-344 D-aminoacylase. Domain 3               1v4yA02 A:61-287,A:345-414 Metal-dependent hydrolases                 -----1v4yA01       ------------------1v4yA01            ---------- CATH domains
               Pfam domains ---------------------------------------------------Amidohydro_3-1v4yA01 A:58-279                                                                                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------D-aminoacyl_C-1v4yA02 A:434-480                 Pfam domains
         Sec.struct. author ...eeee..ee........ee.eeeee..eeeeee.........eee....eeee.eee......hhhhhh..hhhhhh..eeeeee.........ee......hhhhhh.....ee.hhhhhhhhhhhh....eeeeeeehhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeee...hhhhh..hhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhhhh..eee......hhhhh.hhhhhhhhhhhhhhhh.eeeee.....eeee...........eeeeee..hhhhh..hhhhhhhhh..hhhhhhhhhh.eeeee...hhhhhhhhhhh..eee............hhhhhhhhhhhh.........hhhhhhhh.hhhhhhhhh..............eeee....................eeeeee..eeeee..ee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1v4y A   7 PFDYILSGGTVIDGTNAPGRLADVGVRGDRIAAVGDLSASSARRRIDVAGKVVSPGFIDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGISLAPLAHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNAACMVGHSTLRAAVMPDLRREATADEIQAMQALADDALASGAIGISTGAFYPPAAHASTEEIIEVCRPLITHGGVYATAMRDEGEHIVQALEETFRIGRELDVPVVISHHKVMGKLNFGRSKETLALIEAAMASQDVSLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDVVPELQPAGAIYFMMDEPDVQRILAFGPTMIGSDGLPHDERPHPRLWGTFPRVLGHYSRDLGLFPLETAVWKMTGLTAAKFGLAERGQVQPGYYADLVVFDPATVADSATFEHPTERAAGIHSVYVNGAAVWEDQSFTGQHAGRVLNR 480
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       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
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)
(-)
Clan: no clan defined [family: D-aminoacyl_C] (8)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9AGH8_ALCFA | Q9AGH8)
molecular function
    GO:0047420    N-acyl-D-amino-acid deacylase activity    Catalysis of the reaction: H2O + N-acyl-D-amino acid = D-amino acid + an acid.
    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:0016810    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds    Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
    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.

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  3.5.1.81
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 Related Entries

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

UniProtKB/TrEMBL
        Q9AGH8_ALCFA | Q9AGH8: 1m7j 1rjp 1rjq 1rjr 1rk5 1rk6 1v51

(-) Related Entries Specified in the PDB File

1m7j THE SAME PROTEIN IN COMPLEX WITH 100MM ZNCL2
1v51 THE WILD-TYPE PROTEIN