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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE METAL-DEPENDENT HYDROLASE (YP_001302908.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.30 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Nov 09  (Deposition) - 02 Feb 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Putative Metal-Dependent Hydrolase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Metal-Dependent Hydrolase (Yp_001302908. 1) From Parabacteroides Distasonis Atcc 8503 At 2. 30 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE METAL-DEPENDENT HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 26-241
    Gene: BDI_1531
    Organism Scientific: PARABACTEROIDES DISTASONIS ATCC 8503
    Organism Taxid: 435591
    Strain: ATCC 8503 / DSM 20701 / NCTC 11152

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3MSE5Mod. Amino AcidSELENOMETHIONINE
4UNL1Ligand/IonUNKNOWN LIGAND
5ZN2Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , HIS A:81 , HIS A:146 , ASP A:168 , ZN A:303 , HOH A:679BINDING SITE FOR RESIDUE ZN A 302
2AC2SOFTWAREASP A:83 , HIS A:84 , ASP A:168 , HIS A:215 , ZN A:302 , HOH A:679BINDING SITE FOR RESIDUE ZN A 303
3AC3SOFTWAREASP A:218 , THR A:219 , GOL A:308 , HOH A:547 , HOH A:552BINDING SITE FOR RESIDUE ACT A 304
4AC4SOFTWAREGLU A:131 , ILE A:155 , ARG A:162 , ASP A:177 , LYS A:179 , ASP A:234 , ARG A:236 , GOL A:307 , HOH A:610BINDING SITE FOR RESIDUE GOL A 305
5AC5SOFTWARETYR A:50 , SER A:126 , TYR A:127 , LYS A:129 , THR A:157 , ASP A:159 , HOH A:551 , HOH A:559 , HOH A:601BINDING SITE FOR RESIDUE GOL A 306
6AC6SOFTWARELYS A:129 , ARG A:162 , ASP A:180 , ASP A:234 , GOL A:305BINDING SITE FOR RESIDUE GOL A 307
7AC7SOFTWAREVAL A:188 , ASN A:189 , GLN A:190 , MSE A:194 , THR A:195 , VAL A:196 , THR A:219 , ACT A:304 , HOH A:656BINDING SITE FOR RESIDUE GOL A 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KL7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:190 -Pro A:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KL7)

(-) Exons   (0, 0)

(no "Exon" information available for 3KL7)

(-) 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:220
 aligned with A6LC72_PARD8 | A6LC72 from UniProtKB/TrEMBL  Length:241

    Alignment length:220
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
         A6LC72_PARD8    22 NFASDSFKTKSGKELTITFIKHGSLMLTYDNHSIQVDPVSEYADYTTFPKADIILITHEHGDHLDPKAIQAVEKSDTEIIANENSQKKLGKGKVLKNGDTDTSISYMKIEAVPAYNTTPGRDKYHPRHRDNGYILTFDGLRVYIAGDTEDIPEMKDLKDIDIAFLPVNQPYTMTVSQAAKAARMFSPKILYPYHYGDTKIGELKDALKDSGIDVRIRELQ 241
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Lactamase_B_3-3kl7A01 A:37-215                                                                                                                                                     -------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeeeeee..eeeeee..eeeee................eeee........hhhhhhhhh....eeeehhhhhhhhh..ee.....ee......eeeeee......hhhhh......eeeeeee..eeeee......hhhhhhh....eeeee.......hhhhhhhhhhhhh..eeeee.......hhhhhhh.....ee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kl7 A  -3 YFQGDSFKTKSGKELTITFIKHGSLmLTYDNHSIQVDPVSEYADYTTFPKADIILITHEHGDHLDPKAIQAVEKSDTEIIANENSQKKLGKGKVLKNGDTDTSISYmKIEAVPAYNTTPGRDKYHPRHRDNGYILTFDGLRVYIAGDTEDIPEmKDLKDIDIAFLPVNQPYTmTVSQAAKAARmFSPKILYPYHYGDTKIGELKDALKDSGIDVRIRELQ 241
                               ||   31        41     |  51        61        71        81        91       101       111       121      |131       141       151       161       171   |   181       191  |    201   |   211       221       231       241
                               0|                   47-MSE                                                                          128-MSE                                        175-MSE            194-MSE    205-MSE                                
                               26
   Legend:   → Mismatch (orange background)
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  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 3KL7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KL7)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6LC72_PARD8 | A6LC72)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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    Gln A:190 - Pro A:191   [ RasMol ]  
 

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