PDBsum entry 3bbc

Transferase

PDB id: 3bbc

Contents

Protein chain

(+ 0 more) 151 a.a. *

Waters ×1090

* Residue conservation analysis

PDB id:

3bbc

Name:

Transferase

Title:

Crystal structure of r88a mutant of the nm23-h2 transcription factor

Structure:

Nucleoside diphosphate kinase b. Chain: a, b, c, d, e, f. Synonym: ndk b, ndp kinase b, nm23-h2, c-myc purine-binding transcription factor puf. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: nme2, nm23b. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.70Å R-factor: 0.176 R-free: 0.216

Authors:

A.Weichsel,W.R.Montfort

Key ref:

T.S.Dexheimer et al. (2009). NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1). Mol Cancer Ther, 8, 1363-1377. PubMed id: 19435876 DOI: 10.1158/1535-7163.MCT-08-1093

Date:

09-Nov-07 Release date: 23-Sep-08

Protein chains

P22392  (NDKB_HUMAN) -  Nucleoside diphosphate kinase B from Homo sapiens

Seq: 152 a.a.

Struc: 151 a.a.*

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

Enzyme reactions

• Enzyme class 2: E.C.2.7.13.3 - histidine kinase.
• Reaction: ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
• Enzyme class 3: E.C.2.7.4.6 - nucleoside-diphosphate kinase.
• Reaction:
  1. a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-triphosphate + ADP
  2. a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP

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

reference

DOI no: 10.1158/1535-7163.MCT-08-1093

Mol Cancer Ther 8:1363-1377 (2009)

PubMed id: 19435876

NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III(1).

T.S.Dexheimer, S.S.Carey, S.Zuohe, V.M.Gokhale, X.Hu, L.B.Murata, E.M.Maes, A.Weichsel, D.Sun, E.J.Meuillet, W.R.Montfort, L.H.Hurley.

ABSTRACT

The formation of G-quadruplex structures within the nuclease hypersensitive element (NHE) III(1) region of the c-myc promoter and the ability of these structures to repress c-myc transcription have been well established. However, just how these extremely stable DNA secondary structures are transformed to activate c-myc transcription is still unknown. NM23-H2/nucleoside diphosphate kinase B has been recognized as an activator of c-myc transcription via interactions with the NHE III(1) region of the c-myc gene promoter. Through the use of RNA interference, we confirmed the transcriptional regulatory role of NM23-H2. In addition, we find that further purification of NM23-H2 results in loss of the previously identified DNA strand cleavage activity, but retention of its DNA binding activity. NM23-H2 binds to both single-stranded guanine- and cytosine-rich strands of the c-myc NHE III(1) and, to a lesser extent, to a random single-stranded DNA template. However, it does not bind to or cleave the NHE III(1) in duplex form. Significantly, potassium ions and compounds that stabilize the G-quadruplex and i-motif structures have an inhibitory effect on NM23-H2 DNA-binding activity. Mutation of Arg(88) to Ala(88) (R88A) reduced both DNA and nucleotide binding but had minimal effect on the NM23-H2 crystal structure. On the basis of these data and molecular modeling studies, we have proposed a stepwise trapping-out of the NHE III(1) region in a single-stranded form, thus allowing single-stranded transcription factors to bind and activate c-myc transcription. Furthermore, this model provides a rationale for how the stabilization of the G-quadruplex or i-motif structures formed within the c-myc gene promoter region can inhibit NM23-H2 from activating c-myc gene expression. [Mol Cancer Ther 2009;8(5):1363-77].