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(-) Description

Title :  ARCHAEAL DNA HELICASE HJM APO STATE IN FORM 2
 
Authors :  T. Oyama, H. Oka, R. Fujikane, Y. Ishino, K. Morikawa
Date :  29 Feb 08  (Deposition) - 10 Feb 09  (Release) - 10 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Reca Fold, Atp-Binding, Helicase, Hydrolase, Nucleotide- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Oyama, H. Oka, K. Mayanagi, T. Shirai, K. Matoba, R. Fujikane, Y. Ishino, K. Morikawa
Atomic Structures And Functional Implications Of The Archaeal Recq-Like Helicase Hjm
Bmc Struct. Biol. V. 9 2 2009
PubMed-ID: 19159486  |  Reference-DOI: 10.1186/1472-6807-9-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE SKI2-TYPE HELICASE
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: DNA HELICASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2ZJ8)

(-) Sites  (0, 0)

(no "Site" information available for 2ZJ8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJ8)

(-) Sequences/Alignments

Asymmetric 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:700
 aligned with HELS_PYRFU | O73946 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:700
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700
           HELS_PYRFU     1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILYFLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITPFNYSKREFERLEEEYYEFKDRLYFDDPYISGYDPYLERKFFRAFKTALVLLAWINEVPEGEIVEKYSVEPGDIYRIVETAEWLVYSLKEIAKVLGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLG 700
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------DEAD-2zj8A02 A:25-185                                                                                                                                            ---------------------------------------------------------------------------------------------------------Helicase_C-2zj8A03 A:291-373                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HHH-2zj8A01 A:669-698         -- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhh.....hhhhhhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhh..eeee.......hhhhhhh.eeeehhhhhhhhhhhh..hhh.eeeeeee.hhhhhh..hhhhhhhhhhhhh...eeeeee....hhhhhhhhh.eeeee......eeeeeeee..eeee....eee....hhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh....eeee...hhhhh.....eeee...ee......ee.hhhhhhhhhh.........eeeeeee....hhhhhhhhhh............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhh....hhhhhhh.hhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj8 A   1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILYFLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITPFNYSKREFERLEEEYYEFKDRLYFDDPYISGYDPYLERKFFRAFKTALVLLAWINEVPEGEIVEKYSVEPGDIYRIVETAEWLVYSLKEIAKVLGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARALYNSGFRSIEDISQARPEELLKIEGIGVKTVEAIFKFLG 700
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700
   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  (0, 0)

(no "SCOP Domain" information available for 2ZJ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZJ8)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: HHH (112)
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (HELS_PYRFU | O73946)
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: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.
    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: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.

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  HELS_PYRFU | O73946
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  3.6.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        HELS_PYRFU | O73946: 2zj2 2zj5 2zja

(-) Related Entries Specified in the PDB File

2zj2 THE SAME PROTEIN IN ANOTHER CRYSTAL FORM
2zj5 THE SAME PROTEIN IN ANOTHER CRYSTAL FORM
2zja THE SAME PROTEIN COMPLEXED WITH AMPPCP