PDBsum entry 2zig

Transferase

PDB id: 2zig

Contents

Protein chains

236 a.a. *

237 a.a. *

Waters ×160

* Residue conservation analysis

PDB id:

2zig

Name:

Transferase

Title:

Crystal structure of ttha0409, putative DNA modification methylase from thermus thermophilus hb8

Structure:

Putative modification methylase. Chain: a, b. Synonym: ttha0409. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Strain: hb8. Gene: ttha0409. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.233 R-free: 0.274

Authors:

R.Morita,H.Ishikawa,N.Nakagawa,R.Masui,S.Yokoyama,S.Kuramitsu,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

R.Morita et al. (2008). Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8. Proteins, 73, 259-264. PubMed id: 18618709 DOI: 10.1002/prot.22158

Date:

15-Feb-08 Release date: 29-Jul-08

Protein chain

Q5SL84  (Q5SL84_THET8) -  Methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 297 a.a.

Struc: 236 a.a.

Protein chain

Q5SL84  (Q5SL84_THET8) -  Methyltransferase from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 297 a.a.

Struc: 237 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.1.1.- - ?????
• Enzyme class 2: Chains A, B: E.C.2.1.1.113 - site-specific DNA-methyltransferase (cytosine-N(4)-specific).
• Reaction: a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = an N₄-methyl- 2'-deoxycytidine in DNA + S-adenosyl-L-homocysteine + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1002/prot.22158

Proteins 73:259-264 (2008)

PubMed id: 18618709

Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8.

R.Morita, H.Ishikawa, N.Nakagawa, S.Kuramitsu, R.Masui.

ABSTRACT

No abstract given.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of TTHA0409. A: A ribbon model of the overall structure of the ligand-free TTHA0409 dimer (PDB ID; 2ZIG). Rainbow coloring from blue through green to red indicates the N- to C-terminal position of the residue in the model. B: A ribbon model of the monomer structure of TTHA0409. -helices (A-F), -strands (1-10), and TRD are labeled. C: An electrostatic potential map of the ligand-free TTHA0409 dimer. Positively and negatively charged regions are indicated in blue and red, respectively. D: Electrostatic potential map of the active site in the AdoMet-bound TTHA0409 (PDB ID; 2ZIF). E: A ribbon model of the structure of M.RsrI (PDB ID; 1NW5).

Figure 2.
Figure 2. Dimer interface of TTHA0409 (A) and M.MboIIA (B). Each picture on the left shows an enlarged image of the interface including the 4- 5 region in the right picture. In (A), residues 97-115 in one subunit (green) and residues 127-134 in the other subunit (blue) are represented by sticks. Several residues in this region form hydrogen bonds. In (B), residues 74 and 75 in one subunit (green) and residues 89-92 in the other subunit (blue) are represented by sticks. No residue in this region forms a hydrogen bond.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 259-264) copyright 2008.