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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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Crystal structure of human nucleoside diphosphate kinase a
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Structure:
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Nucleoside diphosphate kinase a. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: nm23-h1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
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Biol. unit:
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Hexamer (from
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Resolution:
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2.20Å
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R-factor:
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0.207
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R-free:
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0.263
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Authors:
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K.Min,H.K.Song,C.Chang,S.Y.Kim,K.J.Lee,S.W.Suh
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Key ref:
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K.Min
et al.
(2002).
Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor.
Proteins,
46,
340-342.
PubMed id:
DOI:
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Date:
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10-Sep-01
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Release date:
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10-Apr-02
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PROCHECK
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Headers
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References
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P15531
(NDKA_HUMAN) -
Nucleoside diphosphate kinase A
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Seq:
Struc:
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152 a.a.
149 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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soluble fraction
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9 terms
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Biological process
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cell differentiation
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20 terms
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Biochemical function
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nucleotide binding
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12 terms
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DOI no:
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Proteins
46:340-342
(2002)
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PubMed id:
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Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor.
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K.Min,
H.K.Song,
C.Chang,
S.Y.Kim,
K.J.Lee,
S.W.Suh.
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ABSTRACT
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Selected figure(s)
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Figure 1.
Figure 1. NDK-A hexamer viewed along the threefold axis (top)
and a twofold axis (bottom). Subunits are shown in C  traces,
except one (top) or two subunits (bottom) drawn in ribbon
representation.
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Figure 2.
Figure 2. RMSD plot (gray thick line, between uncomplexed NDK-A
and -B; black line, between uncomplexed NDK-A and GDP-complexed
NDK-B; gray thin line, between uncomplexed NDK-B and
GDP-complexed NDK-B). A pair of hexamer structures are
superimposed for 149 common C atoms
and RMS distances for six subunits are averaged at each residue
position.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2002,
46,
340-342)
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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A.Yamamura,
T.Ichimura,
M.Kamekura,
T.Mizuki,
R.Usami,
T.Makino,
J.Ohtsuka,
K.Miyazono,
M.Okai,
K.Nagata,
and
M.Tanokura
(2009).
Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases.
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Biophys J, 96,
4692-4700.
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PDB code:
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M.Boissan,
S.Dabernat,
E.Peuchant,
U.Schlattner,
I.Lascu,
and
M.L.Lacombe
(2009).
The mammalian Nm23/NDPK family: from metastasis control to cilia movement.
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Mol Cell Biochem, 329,
51-62.
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M.F.Giraud,
F.Georgescauld,
I.Lascu,
and
A.Dautant
(2006).
Crystal structures of S120G mutant and wild type of human nucleoside diphosphate kinase A in complex with ADP.
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J Bioenerg Biomembr, 38,
261-264.
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PDB codes:
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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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Y.Shen,
J.I.Kim,
and
P.S.Song
(2005).
NDPK2 as a signal transducer in the phytochrome-mediated light signaling.
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J Biol Chem, 280,
5740-5749.
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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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V.Anantharaman,
L.Aravind,
and
E.V.Koonin
(2003).
Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins.
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Curr Opin Chem Biol, 7,
12-20.
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H.Yaguchi,
N.Ohkura,
T.Tsukada,
and
K.Yamaguchi
(2002).
Menin, the multiple endocrine neoplasia type 1 gene product, exhibits GTP-hydrolyzing activity in the presence of the tumor metastasis suppressor nm23.
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J Biol Chem, 277,
38197-38204.
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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
