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* Residue conservation analysis
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PDB id:
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Transferase
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Title:
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Mycobacterium tuberculosis nucleoside diphosphate kinase
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Structure:
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Nucleoside diphosphate kinase. Chain: a, b, c, d, e, f. Synonym: ndk, ndp kinase, nucleoside-2-p kinase. Engineered: yes
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Source:
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Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli. Expression_system_taxid: 562
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Biol. unit:
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Hexamer (from
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Resolution:
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2.60Å
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R-factor:
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0.205
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R-free:
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0.246
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Authors:
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Y.Chen,S.Morera,I.Lascu,J.Janin
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Key ref:
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Y.Chen
et al.
(2002).
X-ray structure of Mycobacterium tuberculosis nucleoside diphosphate kinase.
Proteins,
47,
556-557.
PubMed id:
DOI:
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Date:
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05-Oct-01
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Release date:
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15-May-02
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PROCHECK
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Headers
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References
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P84284
(NDK_MYCTU) -
Nucleoside diphosphate kinase
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Seq:
Struc:
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136 a.a.
135 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Enzyme class:
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E.C.2.7.4.6
- Nucleoside-diphosphate kinase.
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Reaction:
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ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
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ATP
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+
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nucleoside diphosphate
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=
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ADP
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+
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nucleoside triphosphate
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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4 terms
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Biological process
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nucleotide metabolic process
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6 terms
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Biochemical function
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nucleotide binding
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10 terms
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DOI no:
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Proteins
47:556-557
(2002)
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PubMed id:
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X-ray structure of Mycobacterium tuberculosis nucleoside diphosphate kinase.
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Y.Chen,
S.Morera,
J.Mocan,
I.Lascu,
J.Janin.
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ABSTRACT
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Selected figure(s)
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Figure 1.
Figure 1. The subunit of M. tuberculosis NDP kinase (blue
ribbon) is superimposed on human NDP kinase B (also called
Nm23-H2, red tube), which is longer by 15 residues at the
C-terminus. Arg4, linked by a salt bridge to the terminal
carboxylate of Ala136, and Ala 97 inserted in the Kpn loop are
drawn in full bonds. A GDP molecule bound to the human B
subunit[6] locates the substrate-binding site.
Both the human and the bacterial enzymes are homo-hexamers.
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The above figure is
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2002,
47,
556-557)
copyright 2002.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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J.Sun,
X.Wang,
A.Lau,
T.Y.Liao,
C.Bucci,
and
Z.Hmama
(2010).
Mycobacterial nucleoside diphosphate kinase blocks phagosome maturation in murine raw 264.7 macrophages.
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PLoS One, 5,
e8769.
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J.D.Pédelacq,
G.S.Waldo,
S.Cabantous,
E.C.Liong,
and
T.C.Terwilliger
(2005).
Structural and functional features of an NDP kinase from the hyperthermophile crenarchaeon Pyrobaculum aerophilum.
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Protein Sci, 14,
2562-2573.
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PDB code:
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P.Kumar,
A.Verma,
A.K.Saini,
P.Chopra,
P.K.Chakraborti,
Y.Singh,
and
S.Chowdhury
(2005).
Nucleoside diphosphate kinase from Mycobacterium tuberculosis cleaves single strand DNA within the human c-myc promoter in an enzyme-catalyzed reaction.
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Nucleic Acids Res, 33,
2707-2714.
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S.Jeudy,
B.Coutard,
R.Lebrun,
and
C.Abergel
(2005).
Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 61,
569-572.
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A.K.Saini,
K.Maithal,
P.Chand,
S.Chowdhury,
R.Vohra,
A.Goyal,
G.P.Dubey,
P.Chopra,
R.Chandra,
A.K.Tyagi,
Y.Singh,
and
V.Tandon
(2004).
Nuclear localization and in situ DNA damage by Mycobacterium tuberculosis nucleoside-diphosphate kinase.
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J Biol Chem, 279,
50142-50149.
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S.Tiwari,
K.V.Kishan,
T.Chakrabarti,
and
P.K.Chakraborti
(2004).
Amino acid residues involved in autophosphorylation and phosphotransfer activities are distinct in nucleoside diphosphate kinase from Mycobacterium tuberculosis.
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J Biol Chem, 279,
43595-43603.
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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.
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Links
