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(-) Description

Title :  ARCHAEAL DNA HELICASE HJM APO STATE IN FORM 1
 
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 :  2.40
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  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:249 , ARG A:344 , THR A:385BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWAREMET A:246 , ARG A:247 , ARG A:248BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWAREARG A:634 , LYS A:638 , TYR A:639BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWARELYS A:108 , HIS A:131 , LYS A:488BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWAREARG A:247 , ALA A:302 , THR A:327 , THR A:329BINDING SITE FOR RESIDUE SO4 A 905

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZJ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZJ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZJ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZJ2)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJ2)

(-) 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:653
 aligned with HELS_PYRFU | O73946 from UniProtKB/Swiss-Prot  Length:720

    Alignment length:664
                                    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    
           HELS_PYRFU     1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLSAGINTPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILYFLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITPFNYSKREFERLEEEYYEFKDRLYFDDPYISGYDPYLERKFFRAFKTALVLLAWINEVPEGEIVEKYSVEPGDIYRIVETAEWLVYSLKEIAKVLGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARALYN 664
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------DEAD-2zj2A01 A:25-185                                                                                                                                            ---------------------------------------------------------------------------------------------------------Helicase_C-2zj2A02 A:291-373                                                       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------       ----------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhh.....hhhhhhhhh.hhhhh.eeeee.hhhhhhhhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhh.eeeeehhhhhhhhhhhhhhhh.eeeeeee.hhhhhh..hhhhhhhhhhhhh...eeeeee....hhhhhhhhh.eeeee.......eeeeeee..eeee....eee...hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh....eeee.....----....eeee...eeee..eeee.hhhhhhhhhh..........eeeeee....hhhhhhhhhh............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..ee.......eehhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhh.............hhhhhhhhhhhhh..........-------hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj2 A   1 MRVDELRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQGGKAVYIVPLKALAEEKFQEFQDWEKIGLRVAMATGDYDSKDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNPEELAEWLNAELIVSDWRPVKLRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRKKKGALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRKGIIKAVVATPTLS----TPAFRVIIRDIWRYSDFGMERIPIIEVHQMLGRAGRPKYDEVGEGIIVSTSDDPREVMNHYIFGKPEKLFSQLSNESNLRSQVLALIATFGYSTVEEILKFISNTFYAYQRKDTYSLEEKIRNILYFLLENEFIEISLEDKIRPLSLGIRTAKLYIDPYTAKMFKDKMEEVVKDPNPIGIFHLISLTPDITPFNYSKREFERLEEEYYEFKDRLYFDDPYI-------ERKFFRAFKTALVLLAWINEVPEGEIVEKYSVEPGDIYRIVETAEWLVYSLKEIAKVLGAYEIVDYLETLRVRVKYGIREELIPLMQLPLVGRRRARALYN 664
                                    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     |   -   |   570       580       590       600       610       620       630       640       650       660    
                                                                                                                                                                                                                                                                                                                                                                    331  336                                                                                                                                                                                                                         556     564
   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 2ZJ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZJ2)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
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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  2zj2
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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: 2zj5 2zj8 2zja

(-) Related Entries Specified in the PDB File

2zj5 THE SAME PROTEIN COMPLEXED WITH ADP
2zj8 THE SAME PROTEIN IN ANOTHER CRYSTAL FORM
2zja THE SAME PROTEIN COMPLEXED WITH AMPPCP