 |
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
 |
|
 |
|
 |
|
|
Gene Ontology (GO) functional annotation
|
|
|
|
 |
 |
 |
|
 |
 |
 |
 |
|
 |
|
Biological process
|
metabolic process
|
2 terms
|
 |
|
Biochemical function
|
catalytic activity
|
6 terms
|
 |
|
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
|
|
| |
|
DOI no:
|
Acta Crystallogr D Biol Crystallogr
60:486-492
(2004)
|
|
PubMed id:
|
|
|
|
|
| |
|
Structure of the biotin carboxylase subunit of pyruvate carboxylase from Aquifex aeolicus at 2.2 A resolution.
|
|
S.Kondo,
Y.Nakajima,
S.Sugio,
J.Yong-Biao,
S.Sueda,
H.Kondo.
|
|
|
|
| |
ABSTRACT
|
|
|
| |
|
Pyruvate carboxylase (PC) is distributed in many eukaryotes as well as in some
prokaryotes. PC catalyzes the ATP-dependent carboxylation of pyruvate to form
oxalacetate. PC has three functional domains, one of which is a biotin
carboxylase (BC) domain. The BC subunit of PC from Aquifex aeolicus (PC-beta)
was crystallized in an orthorhombic form with space group P2(1)2(1)2, unit-cell
parameters a = 92.4, b = 122.1, c = 59.0 A and one molecule in the asymmetric
unit. Diffraction data were collected at 100 K on BL24XU at SPring-8. The
crystal structure was determined by the molecular-replacement method and refined
against 20.0-2.2 A resolution data, giving an R factor of 0.199 and a free R
factor of 0.236. The crystal structure revealed that PC-beta forms a dimeric
quaternary structure consisting of two molecules related by crystallographic
twofold symmetry. The overall structure of PC-beta is similar to other
biotin-dependent carboxylases, such as acetyl-CoA carboxylase (ACC). Although
some parts of domain B were disordered in ACC, the corresponding parts of
PC-beta were clearly determined in the crystal structure. From comparison
between the active-site structure of ACC with ATP bound and a virtual model of
PC-beta with ATP bound, it was shown that the backbone torsion angles of Glu203
in PC-beta change and some of water molecules in the active site of PC-beta are
excluded upon ATP binding.
|
|
|
|
|
| |
Selected figure(s)
|
|
|
| |
 |
 |
|
 |
|
 |
Figure 1.
Figure 1 Overall schematic structure of PC- illustrated
by the program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991).
J. Appl. Cryst. 24, 946-950.]). Domains A, B and C are shown in
red, green and blue, respectively.
|
 |
Figure 2.
Figure 2 Topological diagram of PC- .
Domains A, B and C are shown in red, green and blue,
respectively. The -strands,
-helices
and loop regions are shown by arrows, rectangles and lines,
respectively. The first and last residues are shown as numbers
next to each secondary-structure element.
|
 |
|
|
|
| |
The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2004,
60,
486-492)
copyright 2004.
|
|
| |
Figures were
selected
by an automated process.
|
|
|
|
|
 |
 |
|
 |
 |
 |
 |
 |
 |
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
 |
| |
PubMed id
|
 |
Reference
|
 |
|
|
|
 |
C.Y.Chou,
L.P.Yu,
and
L.Tong
(2009).
Crystal structure of biotin carboxylase in complex with substrates and implications for its catalytic mechanism.
|
| |
J Biol Chem, 284,
11690-11697.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
O.Almog,
A.Kogan,
M.Leeuw,
G.Y.Gdalevsky,
R.Cohen-Luria,
and
A.H.Parola
(2008).
Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41.
|
| |
Biopolymers, 89,
354-359.
|
 |
|
|
|
|
 |
S.Jitrapakdee,
M.St Maurice,
I.Rayment,
W.W.Cleland,
J.C.Wallace,
and
P.V.Attwood
(2008).
Structure, mechanism and regulation of pyruvate carboxylase.
|
| |
Biochem J, 413,
369-387.
|
 |
|
|
|
|
 |
S.O.Nilsson Lill,
J.Gao,
and
G.L.Waldrop
(2008).
Molecular dynamics simulations of biotin carboxylase.
|
| |
J Phys Chem B, 112,
3149-3156.
|
 |
|
|
|
|
 |
S.Xiang,
and
L.Tong
(2008).
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction.
|
| |
Nat Struct Mol Biol, 15,
295-302.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
M.St Maurice,
L.Reinhardt,
K.H.Surinya,
P.V.Attwood,
J.C.Wallace,
W.W.Cleland,
and
I.Rayment
(2007).
Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme.
|
| |
Science, 317,
1076-1079.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
Y.Shen,
C.Y.Chou,
G.G.Chang,
and
L.Tong
(2006).
Is dimerization required for the catalytic activity of bacterial biotin carboxylase?
|
| |
Mol Cell, 22,
807-818.
|
 |
|
PDB codes:
|
 |
|
|
|
|
|
 |
Y.Shen,
S.L.Volrath,
S.C.Weatherly,
T.D.Elich,
and
L.Tong
(2004).
A mechanism for the potent inhibition of eukaryotic acetyl-coenzyme A carboxylase by soraphen A, a macrocyclic polyketide natural product.
|
| |
Mol Cell, 16,
881-891.
|
 |
|
PDB codes:
|
 |
|
|
 |
 |
|
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
codes are
shown on the right.
|
|