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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL XPF/MUS81 HOMOLOG, HEF FROM PYROCOCCUS FURIOSUS, NUCLEASE DOMAIN, CA COCRYSTAL
 
Authors :  T. Nishino, K. Komori, Y. Ishino, K. Morikawa
Date :  25 Dec 02  (Deposition) - 22 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structure-Specific Endonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nishino, K. Komori, Y. Ishino, K. Morikawa
X-Ray And Biochemical Anatomy Of An Archaeal Xpf/Rad1/Mus81 Family Nuclease. Similarity Between Its Endonuclease Domain And Restriction Enzymes
Structure V. 11 445 2003
PubMed-ID: 12679022  |  Reference-DOI: 10.1016/S0969-2126(03)00046-7

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE, PUTATIVE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21DE3 CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEASE DOMAIN FRAGMENT
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638
    Synonym: HEF NUCLEASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:38 , GLU A:48 , ARG A:49 , HOH A:1031 , HOH A:1062 , HOH A:1076 , HOH A:1095BINDING SITE FOR RESIDUE CA A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J24)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J24)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J24)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J24)

(-) Exons   (0, 0)

(no "Exon" information available for 1J24)

(-) Sequences/Alignments

Asymmetric Unit
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:133
 aligned with Q8TZH8_PYRFU | Q8TZH8 from UniProtKB/TrEMBL  Length:764

    Alignment length:133
                                   559       569       579       589       599       609       619       629       639       649       659       669       679   
         Q8TZH8_PYRFU   550 GVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDFIQSIIDGRLFDQVKRLKEAYSRPIMIVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEER 682
               SCOP domains d1j24a_ A: Putative ATP-dependent RNA helicase Hef, nuclease domain                                                                   SCOP domains
               CATH domains 1j24A00 A:4-136  [code=3.40.50.10130, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh.hhhhhhhhhh..eeeee......ee....eeeeeeehhhhhhhhhh.hhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j24 A   4 GVKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEER 136
                                    13        23        33        43        53        63        73        83        93       103       113       123       133
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J24)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | Q8TZH8: 1j22 1j23 1j25 1wp9 1x2i

(-) Related Entries Specified in the PDB File

1j22 XPF/MUS81 HOMOLOG, SELENOMET DERIVATIVE
1j23 XPF/MUS81 HOMOLOG
1j25 XPF/MUS81 HOMOLOG, MN COCRYSTAL