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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL XPF/MUS81 HOMOLOG, HEF FROM PYROCOCCUS FURIOSUS, HELIX-HAIRPIN-HELIX DOMAIN
 
Authors :  T. Nishino, K. Komori, Y. Ishino, K. Morikawa
Date :  24 Apr 05  (Deposition) - 13 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha Helix, Helix-Hairpin-Helix Dna Binding Domain, Homodimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Nishino, K. Komori, Y. Ishino, K. Morikawa
Structural And Functional Analyses Of An Archaeal Xpf/Rad1/Mus81 Nuclease: Asymmetric Dna Binding And Cleavage Mechanisms
Structure V. 13 1183 2005
PubMed-ID: 16084390  |  Reference-DOI: 10.1016/J.STR.2005.04.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEF HELICASE/NUCLEASE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHELIX-HAIRPIN-HELIX DNA BINDING DOMAIN
    GenePF2015
    Organism ScientificPYROCOCCUS FURIOSUS
    Organism Taxid2261
    SynonymATP-DEPENDENT RNA HELICASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1X2I)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 1X2I)

(-) 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:68
 aligned with Q8TZH8_PYRFU | Q8TZH8 from UniProtKB/TrEMBL  Length:764

    Alignment length:68
                                   703       713       723       733       743       753        
         Q8TZH8_PYRFU   694 ALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE 761
               SCOP domains d1x2ia1 A:2-69 ATP-dependent RNA helicase PF2015                     SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1x2i A   2 ALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE  69
                                    11        21        31        41        51        61        

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with Q8TZH8_PYRFU | Q8TZH8 from UniProtKB/TrEMBL  Length:764

    Alignment length:68
                                   703       713       723       733       743       753        
         Q8TZH8_PYRFU   694 ALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE 761
               SCOP domains d1x2ib_ B: ATP-dependent RNA helicase PF2015                         SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------HHH_2-1x2iB01 B:10-69                                        Pfam domains (1)
           Pfam domains (2) --------HHH_2-1x2iB02 B:10-69                                        Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1x2i B   2 ALTLAERQRLIVEGLPHVSATLARRLLKHFGSVERVFTASVAELMKVEGIGEKIAKEIRRVITAPYIE  69
                                    11        21        31        41        51        61        

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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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X2I)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8TZH8_PYRFU | Q8TZH8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8TZH8_PYRFU | Q8TZH81j22 1j23 1j24 1j25 1wp9

(-) Related Entries Specified in the PDB File

1j22 NUCLEASE DOMAIN OF THE SAME PROTEIN
1j23 NUCLEASE DOMAIN OF THE SAME PROTEIN
1j24 NUCLEASE DOMAIN OF THE SAME PROTEIN
1j25 NUCLEASE DOMAIN OF THE SAME PROTEIN
1wp9 HELICASE DOMAIN OF THE SAME PROTEIN