PDBsum entry 1io2

Hydrolase

PDB id

1io2

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Contents

			Protein chain

					213 a.a. *

			Waters ×216

* Residue conservation analysis

PDB id:

1io2

Links

Name:

Hydrolase

Title:

Crystal structure of type 2 ribonuclease h from hyperthermophilic archaeon, thermococcus kodakaraensis kod1

Structure:

Ribonuclease hii. Chain: a. Fragment: residues 1-213. Engineered: yes

Source:

Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Gene: rnhb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å

R-factor:

0.223

R-free:

0.274

Authors:

A.Muroya,D.Tsuchiya,M.Ishikawa,M.Haruki,M.Morikawa

Key ref:

A.Muroya et al. (2001). Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses. Protein Sci, 10, 707-714. PubMed id: 11274461

Date:

28-Dec-00

Release date:

18-Apr-01

PROCHECK

	Headers

	References

Protein chain

O74035 (RNH2_THEKO) - Ribonuclease HII from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

Seq: Struc:					228 a.a. 213 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.3.1.26.4 - ribonuclease H.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Endonucleolytic cleavage to 5'-phosphomonoester.

	Protein Sci 10:707-714 (2001)
PubMed id: 11274461

Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.
A.Muroya, D.Tsuchiya, M.Ishikawa, M.Haruki, M.Morikawa, S.Kanaya, K.Morikawa.

ABSTRACT

The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21177858

M.Figiel, H.Chon, S.M.Cerritelli, M.Cybulska, R.J.Crouch, and M.Nowotny (2011).
The structural and biochemical characterization of human RNase H2 complex reveals the molecular basis for substrate recognition and Aicardi-Goutières syndrome defects.

J Biol Chem, 286, 10540-10550.

PDB code:

3puf

20200253

A.Goulet, M.Pina, P.Redder, D.Prangishvili, L.Vera, J.Lichière, N.Leulliot, H.van Tilbeurgh, M.Ortiz-Lombardia, V.Campanacci, and C.Cambillau (2010).
ORF157 from the archaeal virus Acidianus filamentous virus 1 defines a new class of nuclease.

J Virol, 84, 5025-5031.

PDB codes:

3ii2 3ii3 3ild 3ile

20408915

E.Kanaya, T.Sakabe, N.T.Nguyen, S.Koikeda, Y.Koga, K.Takano, and S.Kanaya (2010).
Cloning of the RNase H genes from a metagenomic DNA library: identification of a new type 1 RNase H without a typical active-site motif.

J Appl Microbiol, 109, 974-983.

20615256

J.Okada, T.Okamoto, A.Mukaiyama, T.Tadokoro, D.J.You, H.Chon, Y.Koga, K.Takano, and S.Kanaya (2010).
Evolution and thermodynamics of slow unfolding of hyperstable monomeric proteins.

BMC Evol Biol, 10, 207.

20673218

K.Zhan, and Z.G.He (2010).
Characterization of a new RNase HII and its essential amino acid residues in the archaeon Sulfolobus tokodaii reveals a regulatory C-terminus.

Biochemistry (Mosc), 75, 930-937.

21095591

M.P.Rychlik, H.Chon, S.M.Cerritelli, P.Klimek, R.J.Crouch, and M.Nowotny (2010).
Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage.

Mol Cell, 40, 658-670.

PDB codes:

3o3f 3o3g 3o3h

19923215

N.M.Shaban, S.Harvey, F.W.Perrino, and T.Hollis (2010).
The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction.

J Biol Chem, 285, 3617-3624.

PDB code:

3kio

20472790

S.Le Laz, A.Le Goaziou, and G.Henneke (2010).
Structure-specific nuclease activities of Pyrococcus abyssi RNase HII.

J Bacteriol, 192, 3689-3698.

19399254

A.Mukaiyama, and K.Takano (2009).
Slow unfolding of monomeric proteins from hyperthermophiles with reversible unfolding.

Int J Mol Sci, 10, 1369-1385.

19015152

H.Chon, A.Vassilev, M.L.DePamphilis, Y.Zhao, J.Zhang, P.M.Burgers, R.J.Crouch, and S.M.Cerritelli (2009).
Contributions of the two accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex.

Nucleic Acids Res, 37, 96.

18977771

K.Takano, R.Higashi, J.Okada, A.Mukaiyama, T.Tadokoro, Y.Koga, and S.Kanaya (2009).
Proline effect on the thermostability and slow unfolding of a hyperthermophilic protein.

J Biochem, 145, 79-85.

19228197

T.Tadokoro, and S.Kanaya (2009).
Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the prokaryotic enzymes.

FEBS J, 276, 1482-1493.

17932924

A.Mukaiyama, Y.Koga, K.Takano, and S.Kanaya (2008).
Osmolyte effect on the stability and folding of a hyperthermophilic protein.

Proteins, 71, 110-118.

17510955

K.Takano, Y.Katagiri, A.Mukaiyama, H.Chon, H.Matsumura, Y.Koga, and S.Kanaya (2007).
Conformational contagion in a protein: structural properties of a chameleon sequence.

Proteins, 68, 617-625.

PDB codes:

2df5 2dfe 2dff 2dfh 2dfi

16880556

D.J.You, H.Chon, Y.Koga, K.Takano, and S.Kanaya (2006).
Crystallization and preliminary crystallographic analysis of type 1 RNase H from the hyperthermophilic archaeon Sulfolobus tokodaii 7.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 781-784.

16650002

H.Chon, T.Tadokoro, N.Ohtani, Y.Koga, K.Takano, and S.Kanaya (2006).
Identification of RNase HII from psychrotrophic bacterium, Shewanella sp. SIB1 as a high-activity type RNase H.

FEBS J, 273, 2264-2275.

16367755

K.Takano, S.Endo, A.Mukaiyama, H.Chon, H.Matsumura, Y.Koga, and S.Kanaya (2006).
Structure of amyloid beta fragments in aqueous environments.

FEBS J, 273, 150-158.

PDB code:

1x1p

16511022

H.Chon, H.Matsumura, Y.Koga, K.Takano, and S.Kanaya (2005).
Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 293-295.

15502360

H.Chon, R.Nakano, N.Ohtani, M.Haruki, K.Takano, M.Morikawa, and S.Kanaya (2004).
Gene cloning and biochemical characterizations of thermostable ribonuclease HIII from Bacillus stearothermophilus.

Biosci Biotechnol Biochem, 68, 2138-2147.

14734815

H.S.Jeong, P.S.Backlund, H.C.Chen, A.A.Karavanov, and R.J.Crouch (2004).
RNase H2 of Saccharomyces cerevisiae is a complex of three proteins.

Nucleic Acids Res, 32, 407-414.

12490712

A.Jäger, R.Samorski, F.Pfeifer, and G.Klug (2002).
Individual gvp transcript segments in Haloferax mediterranei exhibit varying half-lives, which are differentially affected by salt concentration and growth phase.

Nucleic Acids Res, 30, 5436-5443.

16233183

A.Muroya, R.Nakano, N.Ohtani, M.Haruki, M.Morikawa, and S.Kanaya (2002).
Importance of an N-terminal extension in ribonuclease HII from Bacillus stearothermophilus for substrate binding.

J Biosci Bioeng, 93, 170-175.

12358432

E.Bini, V.Dikshit, K.Dirksen, M.Drozda, and P.Blum (2002).
Stability of mRNA in the hyperthermophilic archaeon Sulfolobus solfataricus.

RNA, 8, 1129-1136.

12501157

R.L.Rich, and D.G.Myszka (2002).
Survey of the year 2001 commercial optical biosensor literature.

J Mol Recognit, 15, 352-376.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.