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(-) Description

Title :  STRUCTURE OF XPD FROM THERMOPLASMA ACIDOPHILUM
 
Authors :  J. Kuper, S. C. Wolski, J. J. Truglio, C. Kisker
Date :  23 Apr 08  (Deposition) - 08 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Ner, Tfiih, Helicase, Hydrolase, Atp-Binding, Nucleotide-Binding, Iron Sulfur Cluster (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Wolski, J. Kuper, P. Haenzelmann, J. J. Truglio, D. L. Croteau, B. Van Houten, C. Kisker
Crystal Structure Of The Fes Cluster-Containing Nucleotide Excision Repair Helicase Xpd.
Plos Biol. V. 6 E149 2008
PubMed-ID: 18578568  |  Reference-DOI: 10.1371/JOURNAL.PBIO.0060149

(-) Compounds

Molecule 1 - DNA REPAIR HELICASE RAD3 RELATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: XPD

 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
1CA1Ligand/IonCALCIUM ION
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:88 , CYS A:92 , ILE A:93 , LEU A:94 , CYS A:113 , CYS A:128 , CYS A:164BINDING SITE FOR RESIDUE SF4 A1616
2AC2SOFTWAREGLU A:107 , LYS A:111 , GLU A:159 , ASN A:162 , GLU A:312 , GLU A:315BINDING SITE FOR RESIDUE CA A1617

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VSF)

(-) 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:588
 aligned with XPD_THEAC | Q9HM14 from UniProtKB/Swiss-Prot  Length:602

    Alignment length:593
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594   
            XPD_THEAC     5 YGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFRISVESLNRADREAQAYGDPELSQKIHVSDLIEMIRSALQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASRIIAFSDQDEEKYAAILSPEDGGYMQAACLDPSGILEVLKESKTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILKVKKNTIVYFPSYSLMDRVENRVSFEHMKEYRGIDQKELYSMLKKFRRDHGTIFAVSGGRLSEGINFPGNELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRAGQFRKFIPDMKKTSDPASDIYNFFISAQAR 597
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------DEAD_2-2vsfA01 A:56-233                                                                                                                                                           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Helicase_C_2-2vsfA02 A:440-597                                                                                                                                ------------------ Pfam domains
         Sec.struct. author .eeee........hhhhhhh..........eeeeee.hhhhhhhhhhhhhhhhh.....eee..hhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhheeeehhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....eeeeee.....eeeeee..hhhhhhhhhhheeeee.....hhhhhhhhhh....ee......hhh.eeeeee..........hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...........hhhhhhhhhhhhhhh...eeee..hhhhh.-----....eeee........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhh.....eee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsf A  23 YGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSSTMKIRAIPMQGRVNMCILYRMVDDLHEINAESLAKFCNMKKREVMAGNEAACPYFNFKIRSDETKRFLFDELPTAEEFYDYGERNNVCPYESMKAALPDADIVIAPYAYFLNRSVAEKFLSHWGVSRNQIVIILDEAHNLPDIGRSIGSFRISVESLNRADREAQAYGDPELSQKIHVSDLIEMIRSALQSMVSERCGKGDVRIRFQEFMEYMRIMNKRSEREIRSLLNYLYLFGEYVENEKEKVGKVPFSYCSSVASRIIAFSDQDEEKYAAILSPEDGGYMQAACLDPSGILEVLKESKTIHMSGTLDPFDFYSDITGFEIPFKKIGEIFPPENRYIAYYDGVSSKYDTLDEKELDRMATVIEDIILKVKKNTIVYFPSYSLMDRVENRVSFEHMKEYRGIDQKELYSMLKKFRRDHGTIFAVSGGRLSEG-----NELEMIILAGLPFPRPDAINRSLFDYYERKYGKGWEYSVVYPTAIKIRQEIGRLIRSAEDTGACVILDKRAGQFRKFIPDMKKTSDPASDIYNFFISAQAR 615
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502      |  -  |    522       532       542       552       562       572       582       592       602       612   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                509   515                                                                                                    

   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  (0, 0)

(no "SCOP Domain" information available for 2VSF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XPD_THEAC | Q9HM14)
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:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    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.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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.
biological process
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XPD_THEAC | Q9HM14: 4a15 5h8w

(-) Related Entries Specified in the PDB File

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