Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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Structural insights into the inhibition properties of archaeon citrate synthase from Metallosphaera sedula.

Lee, S.H.Son, H.F.Kim, K.J.

(2019) PLoS One 14: e0212807-e0212807

  • DOI: https://doi.org/10.1371/journal.pone.0212807
  • Primary Citation of Related Structures:  
    6ABX, 6ABY

  • PubMed Abstract: 

    Metallosphaera sedula is a thermoacidophilic archaeon and has an incomplete TCA/glyoxylate cycle that is used for production of biosynthetic precursors of essential metabolites. Citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA/glyoxylate cycle by converting oxaloacetate and acetyl-CoA into citrate and coenzyme A. To elucidate the inhibition properties of MsCS, we determined its crystal structure at 1.7 Å resolution. Like other Type-I CS, MsCS functions as a dimer and each monomer consists of two distinct domains, a large domain and a small domain. The oxaloacetate binding site locates at the cleft between the two domains, and the active site was more closed upon binding of the oxaloacetate substrate than binding of the citrate product. Interestingly, the inhibition kinetic analysis showed that, unlike other Type-I CSs, MsCS is non-competitively inhibited by NADH. Finally, amino acids and structural comparison of MsCS with other Type-II CSs, which were reported to be non-competitively inhibited by NADH, revealed that MsCS has quite unique NADH binding mode for non-competitive inhibition.

  • Organizational Affiliation

    School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Citrate synthase
A, B
378Metallosphaera sedula DSM 5348Mutation(s): 0 
Gene Names: Msed_1522
Find proteins for A4YGX6 (Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2))
Explore A4YGX6 
Go to UniProtKB:  A4YGX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4YGX6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.181α = 93.56
b = 53.522β = 105.73
c = 76.285γ = 102.16
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description