DB code: D00158

CATH domain 3.40.50.1010 : Rossmann fold Catalytic domain
1.10.150.20 : DNA polymerase; domain 1
E.C. 3.1.26.4
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
3.40.50.1010 : Rossmann fold M00055 M00175
1.10.150.20 : DNA polymerase; domain 1 M00055 M00104 M00173 M00175 M00208

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P13319 Ribonuclease H
RNase H
EC 3.1.26.4
NP_049859.1 (Protein)
NC_000866.4 (DNA/RNA sequence)
PF02739 (5_3_exonuc_N)
PF09293 (RNaseH_C)
[Graphical View]

KEGG enzyme name
calf thymus ribonuclease H
endoribonuclease H (calf thymus)
RNase H
RNA*DNA hybrid ribonucleotidohydrolase
hybrid ribonuclease
hybridase
hybridase (ribonuclease H)
ribonuclease H
hybrid nuclease

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P13319 RNH_BPT4 Endonucleolytic cleavage to 5''- phosphomonoester.

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00046 C00001 C00960 C01016
E.C.
Compound Magnesium RNA H2O RNA 5'-phosphate 5'-Phosphomonoester
Type divalent metal (Ca2+, Mg2+) nucleic acids H2O nucleic acids,phosphate group/phosphate ion nucleotide
ChEBI 18420
15377
PubChem 888
22247451
962
1tfrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG_351 Unbound Unbound Unbound
1tfrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [2] & [4]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1tfrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 19;ASP 71;ASP 132;SER 153;ASP 155 ASP 132(Magnesium binding)
1tfrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[2]
p.1103-1105, p.1109
[4]
p.28536

References
[1]
Resource
Comments FUNCTION, AND SEQUENCE OF 1-9
Medline ID 91107694
PubMed ID 1703156
Journal J Biol Chem
Year 1991
Volume 266
Pages 1888-97
Authors Hollingsworth HC, Nossal NG
Title Bacteriophage T4 encodes an RNase H which removes RNA primers made by the T4 DNA replication system in vitro.
Related PDB
Related UniProtKB P13319
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.06 ANGSTROMS)
Medline ID 96270512
PubMed ID 8674116
Journal Cell
Year 1996
Volume 85
Pages 1101-12
Authors Mueser TC, Nossal NG, Hyde CC
Title Structure 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 PDB 1tfr
Related UniProtKB P13319
[3]
Resource
Comments
Medline ID
PubMed ID 8608452
Journal RNA
Year 1996
Volume 2
Pages 289-96
Authors Lapham J, Crothers DM
Title RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9353315
Journal J Biol Chem
Year 1997
Volume 272
Pages 28531-8
Authors Bhagwat M, Meara D, Nossal NG
Title Identification of residues of T4 RNase H required for catalysis and DNA binding.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 9336450
Journal Nucleic Acids Res
Year 1997
Volume 25
Pages 4224-9
Authors Artymiuk PJ, Ceska TA, Suck D, Sayers JR
Title Prokaryotic 5'-3' exonucleases share a common core structure with gamma-delta resolvase.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9808040
Journal Nat Struct Biol
Year 1998
Volume 5
Pages 959-64
Authors Yuan YC, Whitson RH, Liu Q, Itakura K, Chen Y
Title A novel DNA-binding motif shares structural homology to DNA replication and repair nucleases and polymerases.
Related PDB
Related UniProtKB

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.

Created Updated
2004-05-07 2009-02-26