 |
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
| |
|
DOI no:
|
Structure
14:287-298
(2006)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
A versatile conformational switch regulates reactivity in human branched-chain alpha-ketoacid dehydrogenase.
|
|
M.Machius,
R.M.Wynn,
J.L.Chuang,
J.Li,
R.Kluger,
D.Yu,
D.R.Tomchick,
C.A.Brautigam,
D.T.Chuang.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
The dehydrogenase/decarboxylase (E1b) component of the 4 MD human branched-chain
alpha-ketoacid dehydrogenase complex (BCKDC) is a thiamin diphosphate
(ThDP)-dependent enzyme. We have determined the crystal structures of E1b with
ThDP bound intermediates after decarboxylation of alpha-ketoacids. We show that
a key tyrosine residue in the E1b active site functions as a conformational
switch to reduce the reactivity of the ThDP cofactor through interactions with
its thiazolium ring. The intermediates do not assume the often-postulated
enamine state, but likely a carbanion state. The carbanion presumably
facilitates the second E1b-catalyzed reaction, involving the transfer of an acyl
moiety from the intermediate to a lipoic acid prosthetic group in the
transacylase (E2b) component of the BCKDC. The tyrosine switch further remodels
an E1b loop region to promote E1b binding to E2b. Our results illustrate the
versatility of the tyrosine switch in coordinating the catalytic events in E1b
by modulating the reactivity of reaction intermediates.
|
|
|
|
|
|
| |
Selected figure(s)
|
|
|
|
| |
|
|
|
|
Figure 8.
Figure 8. Scheme of hE1b-Catalyzed Reactions Emphasizing
the Role of Tyr113-a as the Central Regulatory Conformational
Switch
(A) Prior to substrate binding, the side chain of
Tyr113-a, the switch turn (indicated by Q112|Y113|R114), and the
adjacent LBD binding region are in the S conformation.
(B)
Substrate binding displaces the Tyr113-a side chain and forces
it into the P conformation, where it establishes a hydrogen bond
to the terminal phosphate group in the ThDP cofactor and
additional interactions with the sulfur in the thiazolium ring
(dashed lines). Simultaneously, the switch turn is remodeled,
whereupon the adjacent LBD binding region adopts a
higher-affinity state for LBD.
(C and D) After, or
concomitant with, (C) decarboxylation, LBD binds to hE1b,
followed by (D) the transfer of an acyl moiety, derived from the
degradation of valine, leucine, or isoleucine to lipoic acid
(LA).
TZ, thiazolium ring; AP, aminopyrimidine ring; B,
general base.
|
|
|
|
|
|
| |
The above figure is
reprinted
by permission from Cell Press:
Structure
(2006,
14,
287-298)
copyright 2006.
|
|
| |
Figure was
selected
by the author.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
Literature references that cite this PDB file's
key reference
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
G.Lu,
H.Sun,
P.She,
J.Y.Youn,
S.Warburton,
P.Ping,
T.M.Vondriska,
H.Cai,
C.J.Lynch,
and
Y.Wang
(2009).
Protein phosphatase 2Cm is a critical regulator of branched-chain amino acid catabolism in mice and cultured cells.
|
| |
J Clin Invest, 119,
1678-1687.
|
|
|
|
|
|
|
O.Okhrimenko,
and
I.Jelesarov
(2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
|
| |
J Mol Recognit, 21,
1.
|
|
|
|
|
|
|
V.I.Bunik,
and
D.Degtyarev
(2008).
Structure-function relationships in the 2-oxo acid dehydrogenase family: substrate-specific signatures and functional predictions for the 2-oxoglutarate dehydrogenase-like proteins.
|
| |
Proteins, 71,
874-890.
|
|
|
|
|
|
|
X.Y.Pei,
C.M.Titman,
R.A.Frank,
F.J.Leeper,
and
B.F.Luisi
(2008).
Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multienzyme complex.
|
| |
Structure, 16,
1860-1872.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
C.L.Berthold,
D.Gocke,
M.D.Wood,
F.J.Leeper,
M.Pohl,
and
G.Schneider
(2007).
Structure of the branched-chain keto acid decarboxylase (KdcA) from Lactococcus lactis provides insights into the structural basis for the chemoselective and enantioselective carboligation reaction.
|
| |
Acta Crystallogr D Biol Crystallogr, 63,
1217-1224.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.Li,
M.Machius,
J.L.Chuang,
R.M.Wynn,
and
D.T.Chuang
(2007).
The two active sites in human branched-chain alpha-keto acid dehydrogenase operate independently without an obligatory alternating-site mechanism.
|
| |
J Biol Chem, 282,
11904-11913.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
M.M.Islam,
R.Wallin,
R.M.Wynn,
M.Conway,
H.Fujii,
J.A.Mobley,
D.T.Chuang,
and
S.M.Hutson
(2007).
A novel branched-chain amino acid metabolon. Protein-protein interactions in a supramolecular complex.
|
| |
J Biol Chem, 282,
11893-11903.
|
|
|
|
|
|
|
V.I.Bunik,
J.V.Schloss,
J.T.Pinto,
G.E.Gibson,
and
A.J.Cooper
(2007).
Enzyme-catalyzed side reactions with molecular oxygen may contribute to cell signaling and neurodegenerative diseases.
|
| |
Neurochem Res, 32,
871-891.
|
|
|
|
|
|
|
W.Versées,
S.Spaepen,
M.D.Wood,
F.J.Leeper,
J.Vanderleyden,
and
J.Steyaert
(2007).
Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase.
|
| |
J Biol Chem, 282,
35269-35278.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
M.Kato,
R.M.Wynn,
J.L.Chuang,
C.A.Brautigam,
M.Custorio,
and
D.T.Chuang
(2006).
A synchronized substrate-gating mechanism revealed by cubic-core structure of the bovine branched-chain alpha-ketoacid dehydrogenase complex.
|
| |
EMBO J, 25,
5983-5994.
|
|
|
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.
|
370 a.a.
329 a.a.
_CL
_MN
