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(-) Description

Title :  CRYSTAL STRUCTURE OF URACIL-DNA GLYCOSYLASE (TM0511) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  16 Apr 04  (Deposition) - 04 May 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Tm0511, Uracil-Dna Glycosylase, Structural Genomics, 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 Uracil-Dna Glycosylase (Tm0511) From Thermotoga Maritima At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URACIL-DNA GLYCOSYLASE TM0511
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0511
    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  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SF41Ligand/IonIRON/SULFUR CLUSTER
3UNL1Ligand/IonUNKNOWN LIGAND

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:18 , CYS A:21 , HIS A:24 , CYS A:89 , CYS A:105BINDING SITE FOR RESIDUE SF4 A 201
2AC2SOFTWAREGLU A:46 , GLY A:47 , HIS A:161 , HOH A:305 , HOH A:319BINDING SITE FOR RESIDUE UNL A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VK2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VK2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VK2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VK2)

(-) Exons   (0, 0)

(no "Exon" information available for 1VK2)

(-) 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:191
 aligned with UDGA_THEMA | Q9WYY1 from UniProtKB/Swiss-Prot  Length:192

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           UDGA_THEMA     1 MYTREELMEIVSERVKKCTACPLHLNRTNVVVGEGNLDTRIVFVGEGPGEEEDKTGRPFVGRAGMLLTELLRESGIRREDVYICNVVKCRPPNNRTPTPEEQAACGHFLLAQIEIINPDVIVALGATALSFFVDGKKVSITKVRGNPIDWLGGKKVIPTFHPSYLLRNRSNELRRIVLEDIEKAKSFIKKE 191
               SCOP domains d1vk2a_ A: Thermophilic uracil-DNA glycosylase                                                                                                                                                  SCOP domains
               CATH domains -1vk2A00 A:2-191 Uracil-DNA Glycosylase, subunit E                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhh.......ee.....eeeee...hhhhhhhh....hhhhhhhhhhhhhh..hhhh.eeee.....hhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhh......hhhhhh...ee.hhh.eeeee.hhhhhhhh.hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk2 A   1 mYTREELmEIVSERVKKCTACPLHLNRTNVVVGEGNLDTRIVFVGEGPGEEEDKTGRPFVGRAGmLLTELLRESGIRREDVYICNVVKCRPPNNRTPTPEEQAACGHFLLAQIEIINPDVIVALGATALSFFVDGKKVSITKVRGNPIDWLGGKKVIPTFHPSYLLRNRSNELRRIVLEDIEKAKSFIKKE 191
                            |      |10        20        30        40        50        60    |   70        80        90       100       110       120       130       140       150       160       170       180       190 
                            |      8-MSE                                                   65-MSE                                                                                                                          
                            1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (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 1VK2)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (UDGA_THEMA | Q9WYY1)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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        UDGA_THEMA | Q9WYY1: 1l9g

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