PDBsum entry 1vpe

Transferase

PDB id: 1vpe

Contents

Protein chain

398 a.a. *

Ligands

ANP

3PG

Metals

_MG

Waters ×226

* Residue conservation analysis

PDB id:

1vpe

Name:

Transferase

Title:

Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium thermotoga maritima

Structure:

Phosphoglycerate kinase. Chain: a. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.198 R-free: 0.288

Authors:

G.Auerbach,R.Huber,M.Graettinger,K.Zaiss,H.Schurig,R.Jaenicke,U.Jacob

Key ref:

G.Auerbach et al. (1997). Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability. Structure, 5, 1475-1483. PubMed id: 9384563 DOI: 10.1016/S0969-2126(97)00297-9

Date:

06-May-97 Release date: 17-Jun-98

Protein chain

P36204  (PGKT_THEMA) -  Bifunctional PGK/TIM from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 654 a.a.

Struc: 398 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.2.3 - phosphoglycerate kinase.
• Pathway: Calvin Cycle (carbon fixation stages)
• Reaction: (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP

(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP (Bound ligand (Het Group name = ANP) matches with 81.25% similarity)

• Enzyme class 3: E.C.5.3.1.1 - triose-phosphate isomerase.
• Reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate

D-glyceraldehyde 3-phosphate (Bound ligand (Het Group name = 3PG) matches with 90.91% similarity) = dihydroxyacetone phosphate

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/S0969-2126(97)00297-9

Structure 5:1475-1483 (1997)

PubMed id: 9384563

Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.

G.Auerbach, R.Huber, M.Grättinger, K.Zaiss, H.Schurig, R.Jaenicke, U.Jacob.

ABSTRACT

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.

Selected figure(s)

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°.

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1475-1483) copyright 1997.

Figure was selected by an automated process.