4OV9

Structure of isopropylmalate synthase binding with alpha-isopropylmalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Subdomain II of alpha-isopropylmalate synthase is essential for activity: inferring a mechanism of feedback inhibition.

Zhang, Z.Wu, J.Lin, W.Wang, J.Yan, H.Zhao, W.Ma, J.Ding, J.Zhang, P.Zhao, G.P.

(2014) J Biol Chem 289: 27966-27978

  • DOI: https://doi.org/10.1074/jbc.M114.559716
  • Primary Citation of Related Structures:  
    4OV4, 4OV9

  • PubMed Abstract: 

    The committed step of leucine biosynthesis, converting acetyl-CoA and α-ketoisovalerate into α-isopropylmalate, is catalyzed by α-isopropylmalate synthase (IPMS), an allosteric enzyme subjected to feedback inhibition by the end product L-leucine. We characterized the short form IPMS from Leptospira biflexa (LbIPMS2), which exhibits a catalytic activity comparable with that of the long form IPMS (LbIPMS1) and has a similar N-terminal domain followed by subdomain I and subdomain II but lacks the whole C-terminal regulatory domain. We found that partial deletion of the regulatory domain of LbIPMS1 resulted in a loss of about 50% of the catalytic activity; however, when the regulatory domain was deleted up to Arg-385, producing a protein that is almost equivalent to the intact LbIPMS2, about 90% of the activity was maintained. Moreover, in LbIPMS2 or LbIPMS1, further deletion of several residues from the C terminus of subdomain II significantly impaired or completely abolished the catalytic activity, respectively. These results define a complete and independently functional catalytic module of IPMS consisting of both the N-terminal domain and the two subdomains. Structural comparison of LbIPMS2 and the Mycobacterium tuberculosis IPMS revealed two different conformations of subdomain II that likely represent two substrate-binding states related to cooperative catalysis. The biochemical and structural analyses together with the previously published hydrogen-deuterium exchange data led us to propose a conformation transition mechanism for feedback inhibition mediated by subdomains I and II that might associated with alteration of the binding affinity toward acetyl-CoA.


  • Organizational Affiliation

    From the Chinese Academy of Sciences Key Laboratory of Synthetic Biology and Shanghai International Travel Healthcare Center, Shanghai Entry-Exit Inspection and Quarantine Bureau, Shanghai 200335, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
isopropylmalate synthase414Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)Mutation(s): 0 
Gene Names: IPMS2LEPBI_I1108leuA2
EC: 2.3.3.13
UniProt
Find proteins for B0SN40 (Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris))
Explore B0SN40 
Go to UniProtKB:  B0SN40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0SN40
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VPM
Query on VPM

Download Ideal Coordinates CCD File 
C [auth A](2S)-2-hydroxy-2-(propan-2-yl)butanedioic acid
C7 H12 O5
BITYXLXUCSKTJS-ZETCQYMHSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.354α = 90
b = 131.354β = 90
c = 46.719γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description