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(-) Description

Title :  CRYSTAL STRUCTURE OF TATD-RELATED DEOXYRIBONUCLEASE (TM0667) FROM THERMOTOGA MARITIMA AT 1.8 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jul 02  (Deposition) - 30 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Tm0667, Tatd-Related Deoxyribonuclease, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Tatd-Related Deoxyribonuclease (Tm0667) From Thermotoga Maritima At 1. 8 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TATD-RELATED DEOXYRIBONUCLEASE
    Chains: A
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0667
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 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
1IPA1Ligand/IonISOPROPYL ALCOHOL
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:10BINDING SITE FOR RESIDUE IPA A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J6O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:89 -Glu A:90
2Cys A:202 -Pro A:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J6O)

(-) Exons   (0, 0)

(no "Exon" information available for 1J6O)

(-) 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:260
 aligned with Q9WZD5_THEMA | Q9WZD5 from UniProtKB/TrEMBL  Length:256

    Alignment length:260
                                1                                                                                                                                                                                                                                                               
                                |    6        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
         Q9WZD5_THEMA     - ----MVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLEDSKKSLDLSKTSDRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAIGETGLDFFRNISPAEVQKRVFVEQIELAGKLNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFIDLGFLLGIGGPVTYPKNEALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGVPEAKVDEATTENARRIFLEVKE 256
               SCOP domains d1j6oa_ A: Hypothetical protein TM0667                                                                                                                                                                                                                               SCOP domains
               CATH domains 1j6oA00 A:-4-255 Metal-dependent hydrolases                                                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...hhhhh.hhhhhhhh.....eeeeeee..hhhhhhhhhhhhh....eeeee..hhhhhhhh..hhhhhhhhhh....eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh......eee.....hhhhhhhhhhhheeeeehhhhhh..hhhhhhhhhhhh...eee........hhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j6o A  -4 HHHHmVDTHAHLHFHQFDDDRNAVISSFEENNIEFVVNVGVNLEDSKKSLDLSKTSDRIFCSVGVHPHDAKEVPEDFIEHLEKFAKDEKVVAIGETGLDFFRNISPAEVQKRVFVEQIELAGKLNLPLVVHIRDAYSEAYEILRTESLPEKRGVIHAFSSDYEWAKKFIDLGFLLGIGGPVTYPKNEALREVVKRVGLEYIVLETDCPFLPPQPFRGKRNEPKYLKYVVETISQVLGVPEAKVDEATTENARRIFLEVKE 255
                                |    5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
                                |                                                                                                                                                                                                                                                               
                                0-MSE
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J6O)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9WZD5_THEMA | Q9WZD5)
molecular function
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.

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