6QSS

Crystal Structure of Ignicoccus islandicus malate dehydrogenase co-crystallized with 10 mM Tb-Xo4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization.

Roche, J.Girard, E.Mas, C.Madern, D.

(2019) J.Struct.Biol. --: --

  • DOI: 10.1016/j.jsb.2019.07.006

  • PubMed Abstract: 
  • The NAD(P)-dependent malate dehydrogenases (MalDHs) and NAD-dependent lactate dehydrogenases (LDHs) are homologous enzymes involved in central metabolism. They display a common protein fold and the same catalytic mechanism, yet have a stringent capac ...

    The NAD(P)-dependent malate dehydrogenases (MalDHs) and NAD-dependent lactate dehydrogenases (LDHs) are homologous enzymes involved in central metabolism. They display a common protein fold and the same catalytic mechanism, yet have a stringent capacity to discriminate between their respective substrates. The MalDH/LDH superfamily is divided into several phylogenetically related groups. It has been shown that the canonical LDHs and LDH-like group of MalDHs are primarily tetrameric enzymes that diverged from a common ancestor. In order to gain understanding of the evolutionary history of the LDHs and MalDHs, the biochemical properties and crystallographic structure of the LDH-like MalDH from the hyperthermophilic archaeon Ignicoccus islandicus (I. isl) were determined. I. isl MalDH recognizes oxaloacetate as main substrate, but it is also able to use pyruvate. Surprisingly, with pyruvate, the enzymatic activity profile looks like that of allosteric LDHs, suggesting a hidden allosteric capacity in a MalDH. The I. isl MalDH tetrameric structure in the apo state is considerably different from those of canonical LDH-like MalDHs and LDHs, representing an alternative oligomeric organization. A comparison with MalDH and LDH counterparts provides strong evidence that the divergence between allosteric and non-allosteric members of the superfamily involves homologs with intermediate, atypical properties.


    Organizational Affiliation

    Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.,Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France. Electronic address: dominique.madern@ibs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Malate dehydrogenase
A, B, C, D
310Ignicoccus islandicus DSM 13165Mutation(s): 0 
Find proteins for A0A0U3FQH7 (Ignicoccus islandicus DSM 13165)
Go to UniProtKB:  A0A0U3FQH7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TB
Query on TB

Download SDF File 
Download CCD File 
A, B, C, D
TERBIUM(III) ION
Tb
HKCRVXUAKWXBLE-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
7MT
Query on 7MT

Download SDF File 
Download CCD File 
A, D
Tb-Xo4
C20 H23 N5 O4 Tb
JWLMJALAUZUFRC-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.892 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 78.486α = 90.00
b = 109.017β = 90.00
c = 151.910γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-16-CE11-0011

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-07-24
    Type: Data collection, Database references