1CSI

A very short hydrogen bond provides only moderate stabilization of an enzyme: inhibitor complex of citrate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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

(1994) Biochemistry 33: 7753-7759

  • Primary Citation of Related Structures:  

  • PubMed 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 s ...

    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.


    Related Citations: 
    • Primary Structure of Porcine Heart Citrate Synthase
      Bloxham, D.P.,Parmelee, D.C.,Kumar, S.,Wade, R.D.,Ericsson, L.H.,Neurath, H.,Walsh, K.A.,Titani, K.
      (1981) Proc.Natl.Acad.Sci.USA 78: 5381
    • Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 Angstroms Resolution
      Remington, S.,Wiegand, G.,Huber, R.
      (1982) J.Mol.Biol. 158: 111
    • Proposed Mechanism for the Condensation Reaction of Citrate Synthase. 1.9-Angstroms Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A
      Karpusas, M.,Branchaud, B.,Remington, S.J.
      (1990) Biochemistry 29: 2213
    • Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzyme A
      Wiegand, G.,Remington, S.,Deisenhofer, J.,Huber, R.
      (1984) J.Mol.Biol. 174: 205
    • Crystal Structure Analysis of the Tetragonal Crystal Form and Preliminary Molecular Model of Pig-Heart Citrate Synthase
      Wiegand, G.,Kukla, D.,Scholze, H.,Jones, T.A.,Huber, R.
      (1979) Eur.J.Biochem. 93: 41


    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CITRATE SYNTHASE
A
435Gallus gallusMutation(s): 0 
Gene Names: CS
EC: 2.3.3.1
Find proteins for P23007 (Gallus gallus)
Go to Gene View: CS
Go to UniProtKB:  P23007
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OAA
Query on OAA

Download SDF File 
Download CCD File 
A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
CMX
Query on CMX

Download SDF File 
Download CCD File 
A
CARBOXYMETHYLDETHIA COENZYME *A
C23 H38 N7 O18 P3
SKRDARVCOPFVCP-GRFIIANRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CMXKi: 1.6 nM BINDINGMOAD
CMXKi: 1.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.400α = 90.00
b = 78.500β = 78.90
c = 58.500γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other