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PDBsum entry 1vpe
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References listed in PDB file
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Key reference
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Title
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Closed structure of phosphoglycerate kinase from thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
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Authors
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G.Auerbach,
R.Huber,
M.Grättinger,
K.Zaiss,
H.Schurig,
R.Jaenicke,
U.Jacob.
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Ref.
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Structure, 1997,
5,
1475-1483.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Phosphoglycerate kinase (PGK) is essential in most living cells both
for ATP generation in the glycolytic pathway of aerobes and for fermentation in
anaerobes. In addition, in many plants the enzyme is involved in carbon
fixation. Like other kinases, PGK folds into two distinct domains, which undergo
a large hinge-bending motion upon catalysis. The monomeric 45 kDa enzyme
catalyzes the transfer of the C1-phosphoryl group from 1, 3-bisphosphoglycerate
to ADP to form 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and
ATP. For decades, the conformation of the enzyme during catalysis has been
enigmatic. The crystal structure of PGK from the hyperthermophilic organism
Thermotoga maritima (TmPGK) represents the first structure of an extremely
thermostable PGK. It adds to a series of four known crystal structures of PGKs
from mesophilic via moderately thermophilic to a hyperthermophilic organism,
allowing a detailed analysis of possible structural determinants of
thermostability. RESULTS: The crystal structure of TmPGK was determined to 2.0 A
resolution, as a ternary complex with the product 3-phosphoglycerate and the
product analogue AMP-PNP (adenylyl-imido diphosphate). The complex crystallizes
in a closed conformation with a drastically reduced inter-domain angle and a
distance between the two bound ligands of 4.4 A, presumably representing the
active conformation of the enzyme. The structure provides new details of the
catalytic mechanism. An inter-domain salt bridge between residues Arg62 and
Asp200 forms a strap to hold the two domains in the closed state. We identify
Lys197 as a residue involved in stabilization of the transition state phosphoryl
group, and so term it the 'phosphoryl gripper'. CONCLUSIONS: The hinge-bending
motion of the two domains upon closure of the structure, as seen in the
Trypanosoma PGK structure, is confirmed. This closed conformation obviously
occurs after binding of both substrates and is locked by the Arg62-Asp200 salt
bridge. Re-orientations in the conserved active-site loop region around Thr374
also bring both domains into direct contact in the core region of the former
inter-domain cleft, to form the complete catalytic site. Comparison of extremely
thermostable TmPGK with less thermostable homologues reveals that its increased
rigidity is achieved by a raised number of intramolecular interactions, such as
an increased number of ion pairs and additional stabilization of alpha helix and
loop regions. The covalent fusion with triosephosphate isomerase might represent
an additional stabilization strategy.
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Figure 3.
Figure 3. Stereo view of the superposition of the closed
structure of TmPGK (black) with the open structure of BsPGK
(red). The central water of the TmPGK structure is shown in
blue. A large motion of residue Thr374 (Thr371; BsPGK) towards
Arg36 causes a subsequent reorientation of the C-terminal
residues Gly375-Gly377 (not labelled). The closed conformation
is locked by an inter-domain salt bridge between Arg62 and
Asp200 (green). The difference between the inter-domain angles
in TmPGK and BsPGK, a[TM] and a[BS], respectively, is 21°.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1475-1483)
copyright 1997.
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Secondary reference #1
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Title
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Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium thermotoga maritima.
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Authors
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G.Auerbach,
U.Jacob,
M.Grättinger,
H.Schurig,
R.Jaenicke.
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Ref.
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Biol Chem, 1997,
378,
327-329.
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PubMed id
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