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(-) Description

Title :  CRYSTAL STRUCTURE OF D-AMINOACYLASE DEFINES A NOVEL SUBSET OF AMIDOHYDROLASES
 
Authors :  S. -H. Liaw, S. -J. Chen, T. -P. Ko, C. -S. Hsu, A. H. -J. Wang, Y. -C. Tsai
Date :  22 Jul 02  (Deposition) - 25 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Tin-Barrel, Metal-Dependent Amidohydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. -H. Liaw, S. -J. Chen, T. -P. Ko, C. -S. Hsu, C. J. Chen, A. H. Wang, Y. -C. Tsai
Crystal Structure Of D-Aminoacylase From Alcaligenes Faecalis Da1. A Novel Subset Of Amidohydrolases And Insights Into The Enzyme Mechanism.
J. Biol. Chem. V. 278 4957 2003
PubMed-ID: 12454005  |  Reference-DOI: 10.1074/JBC.M210795200
(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: PQE
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ALCALIGENES FAECALIS
    Organism Taxid: 511
    Synonym: N-ACYL-D-AMINO ACID AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:96 , HIS A:220 , HIS A:250 , ZN A:802 , ACT A:901BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWAREHIS A:67 , HIS A:69 , CYS A:96 , ASP A:366 , ZN A:801 , ACT A:901BINDING SITE FOR RESIDUE ZN A 802
3AC3SOFTWAREHIS A:67 , HIS A:69 , CYS A:96 , TYR A:192 , HIS A:220 , HIS A:250 , SER A:289 , THR A:290 , ASP A:366 , ZN A:801 , ZN A:802 , ACT A:902BINDING SITE FOR RESIDUE ACT A 901
4AC4SOFTWARELYS A:252 , TYR A:283 , GLY A:288 , SER A:289 , ASP A:366 , ARG A:377 , ACT A:901BINDING SITE FOR RESIDUE ACT A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M7J)

(-) 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 1M7J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M7J)

(-) Exons   (0, 0)

(no "Exon" information available for 1M7J)

(-) 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 d1m7ja1 A:7-61 N-acyl-D-aminoacid amidohydrolase       d1m7ja3 A:62-419 N-acyl-D-aminoacid amidohydrolase, catalytic domain                                                                                                                                                                                                                                                                                                  d1m7ja2 A:420-480 N-acyl-D-aminoacid amidohydrolase           SCOP domains
               CATH domains 1m7jA01 A:7-60,A:420-433,A:452-470                    1m7jA02 A:61-287,A:345-414 Metal-dependent hydrolases                                                                                                                                                                              1m7jA03 A:288-344 D-aminoacylase. Domain 3               1m7jA02 A:61-287,A:345-414 Metal-dependent hydrolases                 -----1m7jA01       ------------------1m7jA01            ---------- CATH domains
               Pfam domains ---------------------------------------------------Amidohydro_3-1m7jA01 A:58-279                                                                                                                                                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------D-aminoacyl_C-1m7jA02 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..eeeee..hhhhh..hhhhhhhhhhhhhhhh.eeeee......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
                 1m7j A   7 PFDYILSGGTVIDGTNAPGRLADVGVRGDRIAAVGDLSASSARRRIDVAGKVVSPGFIDSHTHDDNYLLKHRDMTPKISQGVTTVVTGNCGISLAPLAHANPPAPLDLLDEGGSFRFARFSDYLEALRAAPPAVNAACMVGHSTLRAAVMPDLRREATADEIQAMQALADDALASGAIGISTGAFYPPAAHASTEEIIEVCRPLITHGGVYATHMRDEGEHIVQALEETFRIGRELDVPVVISHHKVMGKLNFGRSKETLALIEAAMASQDVSLDAYPYVAGSTMLKQDRVLLAGRTLITWCKPYPELSGRDLEEIAAERGKSKYDVVPELQPAGAIYFMMDEPDVQRILAFGPTMIGSDGLPHDERPHPRLWGTFPRVLGHYSRDLGLFPLETAVWKMTGLTAAKFGLAERGQVQPGYYADLVVFDPATVADSATFEHPTERAAGIHSVYVNGAAVWEDQSFTGQHAGRVLNR 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)
  - → 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  (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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        Q9AGH8_ALCFA | Q9AGH8: 1rjp 1rjq 1rjr 1rk5 1rk6 1v4y 1v51

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