1J22 - JenaLib

Title :   CRYSTAL STRUCTURE OF ARCHAEAL XPF/MUS81 HOMOLOG, HEF FROM PYROCOCCUS FURIOSUS, NUCLEASE DOMAIN, SELENOMET DERIVATIVE

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 :   1.80

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

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:131
 aligned with Q8TZH8_PYRFU | Q8TZH8 from UniProtKB/TrEMBL  Length:764

    Alignment length:131
                                   560       570       580       590       600       610       620       630       640       650       660       670       680 
         Q8TZH8_PYRFU   551 VKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDFIQSIIDGRLFDQVKRLKEAYSRPIMIVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEE 681
               SCOP domains d1j22a_ A: Putative ATP-dependent RNA helicase Hef, nuclease domain                                                                 SCOP domains
               CATH domains 1j22A00 A:5-135  [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.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j22 A   5 VKVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFDQVKRLKEAYSRPIMIVEGSLYGIRNVHPNAIRGAIAAVTVDFGVPIIFSSTPEETAQYIFLIAKREQEE 135
                                    14        24        34        44        54        64        74        84        94       104       114       124       134

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Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

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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