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(-) Description

Title :  STRUCTURE OF S. TOKODAII XPD4
 
Authors :  J. H. Naismith, K. A. Johnson, M. Oke, S. A. Mcmahon, L. Liu, M. F. White, M. Zawadski, L. G. Carter
Date :  08 Jan 08  (Deposition) - 13 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Helicase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Liu, K. A. Johnson, J. Rudolf, A. -M. Mcrobbie, S. A. Mcmahon, M. Oke, L. G. Carter, J. H. Naismith, M. F. White
Structure Of The Dna Repair Helicase Xpd.
Cell(Cambridge, Mass. ) V. 133 801 2008
PubMed-ID: 18510925  |  Reference-DOI: 10.1016/J.CELL.2008.04.029

(-) Compounds

Molecule 1 - XPD
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET DERIVED
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SULFOLOBUS TOKODAII
    Organism Taxid: 111955
    Strain: 7
    Synonym: UNCHARACTERIZED PROTEIN ST1307

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:35 , GLY A:36 , LEU A:37 , GLY A:38 , LYS A:39BINDING SITE FOR RESIDUE PO4 A1541

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:166 -A:171
2A:244 -A:297
3A:355 -A:518

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VL7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VL7)

(-) Exons   (0, 0)

(no "Exon" information available for 2VL7)

(-) 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:459
 aligned with Q971R4_SULTO | Q971R4 from UniProtKB/TrEMBL  Length:540

    Alignment length:532
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538  
         Q971R4_SULTO     9 RQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQLDSIYKNAKLLGLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLEADKWFTRKISRKMLERALKEIEIVERLNRIDAKKVKDYINLLIDYMSKLIKDGRCHELSLMPLPDRETNGELIVVTRAYLNIDEGPVKKSSLKSLLKFVEMKGDLYNCNGSLVKVPSDVNQLIEDALNVKTFKVLMSGTLPESLTLTNSYKIVVNESYGRGEYYYCPNVTSELRKRNSNIPIYSILLKRIYENSSKSVLVFFPSYEMLESVRIHLSGIPVIEENKKTRHEEVLELMKTGKYLVMLVMRAKESEGVEFREKENLFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRYREYFADLGISEKEIKLFA 540
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------DEAD_2-2vl7A01 A:56-203                                                                                                                             ----------------------------------------------------------------------------------------------------------------------------------------------- ----------------------------Helicase_C_2-2vl7A02 A:376-529                                                                                                                            ----------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhh..eeee---------------------------------------------------------..hhhhh.eeeeehhhhhhhhhhhhhh.......hhh.eeeee.hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh......eeee......hhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..eeeee..eeeee..hhhhhhhhhh.....eeeee...........eeeee....-...eeee......hhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhh......eee.....hhhhhhhhhhh...eeeee.---------------.eeeeeee........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhh..........ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vl7 A   9 RQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQLDSIYKNAKLLGLKTGFL---------------------------------------------------------RANLKDKDVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLEADKWFTRKISRKMLERALKEIEIVERLNRIDAKKVKDYINLLIDYMSKLIKDGRCHELSLMPLPDRETNGELIVVTRAYLNIDEGPVKKSSLKSLLKFVEMKGDLYNCNGSLVKVPSDVNQLIEDALNVKTFKVLMSGTLPESLTLTNSYKIVVNES-GRGEYYYCPNVTSELRKRNSNIPIYSILLKRIYENSSKSVLVFFPSYEMLESVRIHLSGIPVIEENKKTRHEEVLELMKTGKYLVMLVM---------------LFESLVLAGLPYPNVSDDMVRKRIERLSKLTGKDEDSIIHDLTAIVIKQTIGRAFRDPNDYVKIYLCDSRYREYFADLGISEKEIKLFA 540
                                    18        28        38        48        58        68        78  |      -         -         -         -         -         -|      148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       | -         -   |   458       468       478       488       498       508       518       528       538  
                                                                                                   81                                                       139                                                                                                                                                                                                            346 |                                                                                     436             452                                                                                        
                                                                                                                                                                                                                                                                                                                                                                             348
   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 2VL7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VL7)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q971R4_SULTO | Q971R4)
molecular function
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
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:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

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  2vl7
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