4OV4

Isopropylmalate synthase binding with ketoisovalerate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


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

  • 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 ...

    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 Key Laboratory of Medical Molecular Virology affiliated to the Ministries of Education and Health, Shanghai Medical College, and Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China, Shanghai-Ministry of Science and Technology Key Laboratory for Health and Disease Genomics, Chinese National Human Genome Center, Shanghai 201203, China, Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region 999077, China, and gpzhao@sibs.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-isopropylmalate synthaseA414Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)Mutation(s): 0 
Gene Names: IPMS2LEPBI_I1108leuA2
EC: 2.3.3.13
Find proteins for B0SN40 (Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris))
Explore B0SN40 
Go to UniProtKB:  B0SN40
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KIV
Query on KIV

Download Ideal Coordinates CCD File 
C [auth A]3-METHYL-2-OXOBUTANOIC ACID
C5 H8 O3
QHKABHOOEWYVLI-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.937α = 90
b = 129.937β = 90
c = 46.693γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report



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