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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL HALF OF ARCHAEOGLOBUS FULGIDUS XPB
 
Authors :  L. Fan, J. A. Tainer
Date :  09 Feb 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Reca-Like Domain, Dna Damage Recognition Domain, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Fan, A. S. Arvai, P. K. Cooper, S. Iwai, F. Hanaoka, J. A. Tainer
Conserved Xpb Core Structure And Motifs For Dna Unwinding: Implications For Pathway Selection Of Transcription Or Excision Repair.
Mol. Cell V. 22 27 2006
PubMed-ID: 16600867  |  Reference-DOI: 10.1016/J.MOLCEL.2006.02.017

(-) Compounds

Molecule 1 - DNA REPAIR PROTEIN RAD25
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL HALF
    Gene: RAD25
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2FZ4)

(-) Sites  (0, 0)

(no "Site" information available for 2FZ4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FZ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FZ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FZ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FZ4)

(-) Exons   (0, 0)

(no "Exon" information available for 2FZ4)

(-) 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:206
 aligned with O29889_ARCFU | O29889 from UniProtKB/TrEMBL  Length:452

    Alignment length:206
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203      
         O29889_ARCFU     4 IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFE 209
               SCOP domains d2fz4a1 A:24-229 DNA repair protein RAD25                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeee........eee....eeeee..hhhhhhhhhhhh...eeee................hhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh...eeeee.hhhhhhhhhh.hhhhhhh.eeee.........eeeeehhhhhhhhhhhh....eeeee........hhhhhhhh....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fz4 A  24 IAEIYYERGTIVVKGDAHVPHAKFDSRSGTYRALAFRYRDIIEYFESNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINELSTPTLIVVPTLALAEQWKERLGIFGEEYVGEFSGRIKELKPLTVSTYDSAYVNAEKLGNRFMLLIFDEVHHLPAESYVQIAQMSIAPFRLGLTATFE 229
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FZ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FZ4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O29889_ARCFU | O29889)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic 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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

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 Related Entries

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

UniProtKB/TrEMBL
        O29889_ARCFU | O29889: 2fwr 2fzl

(-) Related Entries Specified in the PDB File

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