PDBsum entry: 1wpk

DNA binding protein

PDB id: 1wpk

Contents

Protein chain

146 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

1wpk

Name:

DNA binding protein

Title:

Methylated form of n-terminal transcriptional regulator domain of escherichia coli ada protein

Structure:

Ada regulatory protein. Chain: a. Fragment: methylated n-terminal 16 kda domain. Synonym: regulatory protein of adaptative response. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ada. Expressed in: escherichia coli k12. Expression_system_taxid: 83333.

NMR struc:

17 models

Authors:

H.Takinowaki,Y.Matsuda,T.Yoshida,Y.Kobayashi,T.Ohkubo

Key ref:

H.Takinowaki et al. (2006). The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein. Protein Sci, 15, 487-497. PubMed id: 16452614 DOI: 10.1110/ps.051786306

Date:

07-Sep-04 Release date: 13-Sep-05

Protein chain

P06134  (ADA_ECOLI) -  Bifunctional transcriptional activator/DNA repair enzyme Ada

Seq: 354 a.a.

Struc: 146 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 1: E.C.2.1.1 - Guanidinoacetate N-methyltransferase.
• Pathway: Creatine Biosynthesis
• Reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine
• Enzyme class 2: E.C.2.1.1.63 - Methylated-DNA--[protein]-cysteine S-methyltransferase.
• Reaction: DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine

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

 Gene Ontology (GO) functional annotation 

• Cellular component: intracellular (1 term)
• Biological process: DNA repair (2 terms)
• Biochemical function: protein binding (6 terms)

reference

DOI no: 10.1110/ps.051786306

Protein Sci 15:487-497 (2006)

PubMed id: 16452614

The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein.

H.Takinowaki, Y.Matsuda, T.Yoshida, Y.Kobayashi, T.Ohkubo.

ABSTRACT

The N-terminal 16-kDa domain of Escherichia coli Ada protein (N-Ada16k) repairs DNA methyl phosphotriester lesions by an irreversible methyl transfer to its cysteine residue. Upon the methylation, the sequence-specific DNA binding affinity for the promoter region of the alkylation resistance genes is enhanced by 10(3)-fold. Then, it acts as a transcriptional regulator for the methylation damage. In this paper, we identified the methyl acceptor residue of N-Ada16k and determined the solution structure of the methylated form of N-Ada16k by using NMR and mass spectrometry. The results of a 13C-filtered 1H-13C HMBC experiment and MALDI-TOF MS and MS/MS experiments clearly showed that the methyl acceptor residue is Cys38. The solution structure revealed that it has two distinct subdomains connected by a flexible linker loop: the methyltransferase (MTase) subdomain with the zinc-thiolate center, and the helical subdomain with a helix-turn-helix motif. Interestingly, there is no potential hydrogen bond donor around Cys38, whereas the other three cysteine residues coordinated to a zinc ion have potential donors. Hence, Cys38 could retain its inherent nucleophilicity and react with a methyl phosphotriester. Furthermore, the structure comparison shows that there is no indication of a remarkable conformational change occurring upon the methylation. This implies that the electrostatic repulsion between the negatively charged DNA and the zinc-thiolate center may avoid the contact between the MTase subdomain and the DNA in the nonmethylated form. Thus, after the Cys38 methylation, the MTase subdomain can bind the cognate DNA because the negative charge of the zinc-thiolate center is reduced.

Selected figure(s)

Figure 1.
2D ^13C-filtered ^1H-^13C HMBC spectrum of the methylated form of N-Ada16k.

Figure 6.
Protein surfaces of the nonmethylated (left, PDB accession code 1EYF) and the methylated (right, PDB accession code 1WPK) forms of the MTase subdomain. The basic residues with and without the chemical shift perturbations upon the DNA binding are colored blue and sky blue, respectively. The hydrophobic residues are colored dark orange. The hydrophobic residues in Figure 3D 3D Figure 3.-(Val31 and Ile36) are colored orange red. The methyl acceptor residue (Cys38) and the other three cysteine residues (Cys42, Cys69, and Cys72) are colored green and yellow, respectively. In the methylated form, the S[gamma]-methyl group of Cys38 is colored pink.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2006, 15, 487-497) copyright 2006.

Figures were selected by an automated process.