PDBsum entry 2fpp

Ligase

PDB id: 2fpp

Contents

Protein chains

305 a.a. *

393 a.a. *

Ligands

SO4 ×3

Metals

_CL

Waters ×126

* Residue conservation analysis

PDB id:

2fpp

Name:

Ligase

Title:

Crystal structure of pig gtp-specific succinyl-coa synthetase from polyethylene glycol with chloride ions

Structure:

Succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial. Chain: a. Synonym: succinyl-coa synthetase, alpha chain, scs-alpha. Engineered: yes. Succinyl-coa ligase [gdp-forming] beta-chain, mitochondrial. Chain: b. Synonym: succinyl-coa synthetase, betag chain, scs-betag, gtp-

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: suclg1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: suclg2.

Biol. unit:

Dimer (from PQS)

Resolution:

2.35Å R-factor: 0.192 R-free: 0.259

Authors:

M.E.Fraser,K.Hayakawa,M.S.Hume,D.G.Ryan,E.R.Brownie

Key ref:

M.E.Fraser et al. (2006). Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase. J Biol Chem, 281, 11058-11065. PubMed id: 16481318 DOI: 10.1074/jbc.M511785200

Date:

16-Jan-06 Release date: 21-Feb-06

Protein chain

O19069  (SUCA_PIG) -  Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial from Sus scrofa

Seq: 346 a.a.

Struc: 305 a.a.*

Protein chain

P53590  (SUCB2_PIG) -  Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial (Fragment) from Sus scrofa

Seq: 433 a.a.

Struc: 393 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.6.2.1.4 - succinate--CoA ligase (GDP-forming).
• Pathway: Citric acid cycle
• Reaction: GTP + succinate + CoA = succinyl-CoA + GDP + phosphate
• Enzyme class 2: Chain A: E.C.6.2.1.5 - succinate--CoA ligase (ADP-forming).
• Reaction: succinate + ATP + CoA = succinyl-CoA + ADP + 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: 10.1074/jbc.M511785200

J Biol Chem 281:11058-11065 (2006)

PubMed id: 16481318

Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.

M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, E.R.Brownie.

ABSTRACT

Two isoforms of succinyl-CoA synthetase exist in mammals, one specific for ATP and the other for GTP. The GTP-specific form of pig succinyl-CoA synthetase has been crystallized in the presence of GTP and the structure determined to 2.1 A resolution. GTP is bound in the ATP-grasp domain, where interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity. The gamma-phosphate interacts with the side chain of an arginine residue (Arg-54beta) and with backbone amide nitrogen atoms, leading to tight interactions between the gamma-phosphate and the protein. This contrasts with the structures of ATP bound to other members of the family of ATP-grasp proteins where the gamma-phosphate is exposed, free to react with the other substrate. To test if GDP would interact with GTP-specific succinyl-CoA synthetase in the same way that ADP interacts with other members of the family of ATP-grasp proteins, the structure of GDP bound to GTP-specific succinyl-CoA synthetase was also determined. A comparison of the conformations of GTP and GDP shows that the bases adopt the same position but that changes in conformation of the ribose moieties and the alpha- and beta-phosphates allow the gamma-phosphate to interact with the arginine residue and amide nitrogen atoms in GTP, while the beta-phosphate interacts with these residues in GDP. The complex of GTP with succinyl-CoA synthetase shows that the enzyme is able to protect GTP from hydrolysis when the active-site histidine residue is not in position to be phosphorylated.

Selected figure(s)

Figure 1.
FIGURE 1. A, ribbon diagram of pig GTP-specific SCS showing the location of the GTP-binding site. The -subunit is green, the -subunit is yellow, except for the T-loop, which is highlighted in magenta. GTP, the potassium ion, and the side chain of the phosphorylated histidine residue, His-259 , are drawn as stick models and colored according to atom type: red for oxygen, yellow for carbon, blue for nitrogen, green for phosphorus, and turquoise for potassium. B, stereo view of the electron density for GTP and the potassium ion, including nearby residues of the ATP-grasp domain of pig GTP-specific SCS. The F[o] - F[c], [c] electron density map calculated without GTP and the potassium ion is contoured at 3 . C, stereo view of the electron density for GDP and the potassium ion, including nearby residues of the ATP-grasp domain of pig GTP-specific SCS. The F[o] - F[c], [c] electron density map calculated without GDP and the potassium ion is contoured at 3 . The same atom colors were used in B and C as described for A. All parts of the figure were drawn using the program RASTER3D (58), and B and C also used the program XFIT (47).

Figure 3.
FIGURE 3. Stereo views of the superpositions of GTP bound to pig GTP-specific SCS (black) with ADP bound to E. coli SCS (gray) (Protein Data Bank (43) identifier 1cqi (7)) (A), GDP bound to pig GTP-specific SCS (gray) (B), and ATP bound to glycinamide ribonucleotide transformylase (gray) (PDB identifier 1kj8) (54) (C). The superpositions were based on structurally similar residues and performed using the program O (51) with a cutoff of 3.8 Å. Possible hydrogen-bonding interactions and ionic interactions between GTP and the pig GTP-specific SCS are represented by black dashed lines.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 11058-11065) copyright 2006.

Figures were selected by the author.