PDBsum entry 1csh

Lyase(oxo-acid)

PDB id: 1csh

Contents

Protein chain

435 a.a.

Ligands

OAA

AMX

Waters ×145

References listed in PDB file

Key reference

Title

A very short hydrogen bond provides only moderate stabilization of an enzyme-Inhibitor complex of citrate synthase.

Authors

K.C.Usher, S.J.Remington, D.P.Martin, D.G.Drueckhammer.

Ref.

Biochemistry, 1994, 33, 7753-7759. [DOI no: 10.1021/bi00191a002]

PubMed id

8011640

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 91%.

Abstract

Two extremely potent inhibitors of citrate synthase, carboxyl and primary amide analogues of acetyl coenzyme A, have been synthesized. The ternary complexes of these inhibitors with oxaloacetate and citrate synthase have been crystallized and their structures analyzed at 1.70- and 1.65-A resolution, respectively. The inhibitors have dissociation constants in the nanomolar range, with the carboxyl analogue binding more tightly (Ki = 1.6 nM at pH 6.0) than the amide analogue (28 nM), despite the unfavorable requirement for proton uptake by the former. The carboxyl group forms a shorter hydrogen bond with the catalytic Asp 375 (distance < 2.4 A) than does the amide group (distance approximately 2.5 A). Particularly with the carboxylate inhibitor, the very short hydrogen bond distances measured suggest a low barrier or short strong hydrogen bond. However, the binding constants differ by only a factor of 20 at pH 6.0, corresponding to an increase in binding energy for the carboxyl analogue on the enzyme of about 2 kcal/mol more than the amide analogue, much less than has been proposed for short strong hydrogen bonds based on gas phase measurements [> 20 kcal/mol (Gerlt & Gassman, 1993a,b)]. The inhibitor complexes support proposals that Asp 375 and His 274 work in concert to form an enolized form of acetyl-coenzyme A as the first step in the reaction.

Secondary reference #1

Title

Proposed mechanism for the condensation reaction of citrate synthase: 1.9-A structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme a.

Authors

M.Karpusas, B.Branchaud, S.J.Remington.

Ref.

Biochemistry, 1990, 29, 2213-2219. [DOI no: 10.1021/bi00461a002]

PubMed id

2337600

Secondary reference #2

Title

Crystal structure analysis and molecular model of a complex of citrate synthase with oxaloacetate and s-Acetonyl-Coenzyme a.

Authors

G.Wiegand, S.Remington, J.Deisenhofer, R.Huber.

Ref.

J Mol Biol, 1984, 174, 205-219. [DOI no: 10.1016/0022-2836(84)90373-5]

PubMed id

6716477

Figure 2.
FIG. 2. The small omains of the closed form (C2) and the closed form (P4,2,2) are optimally superimposed and shown in the stereo diagram. The conformations also differ substantially for internal residues as ndicated specifically for some residues.

The above figure is reproduced from the cited reference with permission from Elsevier

Secondary reference #3

Title

Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1.7 a resolution.

Authors

S.Remington, G.Wiegand, R.Huber.

Ref.

J Mol Biol, 1982, 158, 111-152. [DOI no: 10.1016/0022-2836(82)90452-1]

PubMed id

7120407

Figure 1.
BVIE

Figure 19.
FIG. 19. Stereo drawing of the citryl-thioether-CoA analogue ((XC%NPH6) difference Fourier map superimposed on the monoclinic model. Contours are at +49 e. with negative contours dashed. The Figure is discussd in the text.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #4

Title

Primary structure of porcine heart citrate synthase.

Authors

D.P.Bloxham, D.C.Parmelee, S.Kumar, R.D.Wade, L.H.Ericsson, H.Neurath, K.A.Walsh, K.Titani.

Ref.

Proc Natl Acad Sci U S A, 1981, 78, 5381-5385. [DOI no: 10.1073/pnas.78.9.5381]

PubMed id

6795632

Secondary reference #5

Title

Crystal structure analysis of the tetragonal crystal form are preliminary molecular model of pig-Heart citrate synthase.

Authors

G.Wiegand, D.Kukla, H.Scholze, T.A.Jones, R.Huber.

Ref.

Eur J Biochem, 1979, 93, 41-50.

PubMed id

436830