DB code: D00158

CATH domain	3.40.50.1010 : Rossmann fold	Catalytic domain
CATH 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)
1.10.150.20 : DNA polymerase; domain 1	M00055 M00104 M00173 M00175 M00208
3.40.50.1010 : Rossmann fold	M00055 M00175

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 18420		15377 15377
PubChem	888 888		22247451 962 22247451 962

1tfrA01	Bound:_MG_351	Unbound		Unbound	Unbound
1tfrA02	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	ASP 19;ASP 71;ASP 132;SER 153;ASP 155	ASP 132(Magnesium binding)
1tfrA02

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.

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