1IOM

CRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM THERMUS THERMOPHILUS HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8.

Kanamori, E.Kawaguchi, S.Kuramitsu, S.Kouyama, T.Murakami, M.

(2015) Biophys Physicobiol 12: 47-56

  • DOI: 10.2142/biophysico.12.0_47
  • Primary Citation of Related Structures:  
    1IOM, 1IXE

  • PubMed Abstract: 
  • The crystal structures of citrate synthase from the thermophilic eubacteria Thermus thermophilus HB8 (TtCS) were determined for an open form at 1.5 Å resolution and for closed form at 2.3 Å resolution, respectively. In the absence of ligands TtCS in ...

    The crystal structures of citrate synthase from the thermophilic eubacteria Thermus thermophilus HB8 (TtCS) were determined for an open form at 1.5 Å resolution and for closed form at 2.3 Å resolution, respectively. In the absence of ligands TtCS in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. TtCS was also co-crystallized with citrate and coenzyme-A to form an orthorhombic crystal with two homodimers in the asymmetric unit. Citrate and CoA are found in the active site situated between the large domain and the small domain in all subunit whereas the complex shows two distinct closed conformations, the fully closed form and partially closed form. Structural comparisons are performed to describe conformational changes associated with binding of products of TtCS. Upon binding of citrate, basic residues in the active site move toward citrate and make a hydrogen bond network in the active site, inducing a large-scale rotation of the small domain relative to the large domain. CoA is sandwiched between the small and large domains and then the cysteamine tail is inserted into the active site with a cooperative rotation around mainchain dihedrals in the hinge region connecting helices M and N. According to this rotation these helices are extended to close the active site completely. The considerable flexibility and structural rearrangements in the hinge region are crucial for an ordered bibi reaction in catalysis for microbial CSs.


    Organizational Affiliation

    Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CITRATE SYNTHASEA377Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA1343
EC: 4.1.3.7
Find proteins for Q5SIM6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SIM6 
Go to UniProtKB:  Q5SIM6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.55α = 90
b = 84.55β = 90
c = 153.52γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2015-11-04
    Changes: Database references
  • Version 1.5: 2020-01-01
    Changes: Advisory, Database references