EzCatDB: D00158

DB codeD00158
CATH domainDomain 13.40.50.1010Catalytic domain
Domain 21.10.150.20
E.C.3.1.26.4

CATH domainRelated DB codes (homologues)
1.10.150.20M00055,M00104,M00173,M00175,M00208
3.40.50.1010M00055,M00175

Enzyme Name
Swiss-protKEGG

P13319
Protein nameRibonuclease Hcalf thymus ribonuclease H
endoribonuclease H (calf thymus)
RNase H
RNA*DNA hybrid ribonucleotidohydrolase
hybrid ribonuclease
hybridase
hybridase (ribonuclease H)
ribonuclease H
hybrid nuclease
SynonymsRNase H
EC 3.1.26.4


Swiss-prot:Accession NumberP13319
Entry nameRNH_BPT4
ActivityEndonucleolytic cleavage to 5''- phosphomonoester.
Subunit
Subcellular location
Cofactor


CofactorsSubstratesProducts
KEGG-idC00305C00046C00001C00960C01016
CompoundMagnesiumRNAH2ORNA 5'-phosphate5'-Phosphomonoester
Typedivalent metal (Ca2+, Mg2+)nucleic acidsH2Onucleic acids,phosphate group/phosphate ionnucleotide
1tfrA01Bound:_MG 351Unbound
UnboundUnbound
1tfrA02UnboundUnbound
UnboundUnbound

Active-site residues
resource
literature [2] & [4]
pdbCatalytic residuesCofactor-binding residues
1tfrA01ASP 19;ASP 71;ASP 132;SER 153;ASP 155
ASP 132(Magnesium binding)
1tfrA02


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.1103-1105, p.1109
[4]p.28536

references
[1]
CommentsFUNCTION, AND SEQUENCE OF 1-9
Medline ID91107694
PubMed ID1703156
JournalJ Biol Chem
Year1991
Volume266
Pages1888-97
AuthorsHollingsworth HC, Nossal NG
TitleBacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro.
Related Swiss-protP13319
[2]
CommentsX-RAY CRYSTALLOGRAPHY (2.06 ANGSTROMS)
Medline ID96270512
PubMed ID8674116
JournalCell
Year1996
Volume85
Pages1101-12
AuthorsMueser TC, Nossal NG, Hyde CC
TitleStructure of bacteriophage T4 RNase H, a 5' to 3' RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins.
Related PDB1tfr
Related Swiss-protP13319
[3]
PubMed ID8608452
JournalRNA
Year1996
Volume2
Pages289-96
AuthorsLapham J, Crothers DM
TitleRNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation.
[4]
PubMed ID9353315
JournalJ Biol Chem
Year1997
Volume272
Pages28531-8
AuthorsBhagwat M, Meara D, Nossal NG
TitleIdentification of residues of T4 RNase H required for catalysis and DNA binding.
[5]
PubMed ID9336450
JournalNucleic Acids Res
Year1997
Volume25
Pages4224-9
AuthorsArtymiuk PJ, Ceska TA, Suck D, Sayers JR
TitleProkaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.
[6]
PubMed ID9808040
JournalNat Struct Biol
Year1998
Volume5
Pages959-64
AuthorsYuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
TitleA novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.

comments
According to the literature [2] & [4], the catalytic residues have been identified for this enzyme, but its catalytic mechanism has not been elucidated yet.
According to the literature [2] & [4], of the two magnesium ions bound to this enzyme, the first one, Mg2+-1, which is coordinated to the sidechain of Asp132, seems to be involved in catalysis. Moreover, the sidechains of Asp19, Asp71, Asp155 also interact with Mg2+-1 through four water molecules. According to the paper [4], Ser153 might be involved in catalysis.

createdupdated
2004-05-072009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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