6IHE

Crystal structure of Malate dehydrogenase from Metallosphaera sedula


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure and biochemical characterization of malate dehydrogenase from Metallosphaera sedula

Lee, D.Hong, J.Kim, K.J.

(2019) Biochem Biophys Res Commun 509: 833-838

  • DOI: 10.1016/j.bbrc.2019.01.018
  • Primary Citation of Related Structures:  
    6IHD, 6IHE

  • PubMed Abstract: 
  • Metallosphaera sedula is a thermoacidophilic autotrophic archaeon and known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as a carbon fixation pathway. The 3-HP/4-HB cycle in M. sedula is associated with central metabolism, and malate dehydrogenase (MDH) is an enzyme involved in the central metabolism that converts malate to oxaloacetate ...

    Metallosphaera sedula is a thermoacidophilic autotrophic archaeon and known to utilize the 3-hydroxypropionate/4-hydroxybutyrate cycle (3-HP/4-HB cycle) as a carbon fixation pathway. The 3-HP/4-HB cycle in M. sedula is associated with central metabolism, and malate dehydrogenase (MDH) is an enzyme involved in the central metabolism that converts malate to oxaloacetate. To elucidate the enzymatic properties of MDH from M. sedula (MsMDH), we determined the crystal structure of MsMDH as a complex with NAD + and a ternary complex with malate and NAD + . Based on its complex structures and biochemical experiments, we observed that MsMDH can utilize both NAD + and NADP + as a cofactor. In addition, we revealed that MsMDH shows a conformational change at the active site upon substrate binding. Based on the comparison with other MDHs, we revealed that MsMDH was distinguished from general MDHs due to a Lys80 residue, and this difference is likely to influence the unique cofactor specificity of MsMDH.


    Organizational Affiliation

    School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 702-701, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea. Electronic address: kkim@knu.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Malate dehydrogenase (NAD)A, B303Metallosphaera sedulaMutation(s): 0 
Gene Names: Msed_0455HA72_0455MsedA_0468MsedB_0468MsedC_0467MsedD_0468MsedE_0468
EC: 1.1.1.37
UniProt
Find proteins for A0A088E2H7 (Metallosphaera sedula)
Explore A0A088E2H7 
Go to UniProtKB:  A0A088E2H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A088E2H7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
L [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
O [auth B],
P [auth B],
Q [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
MLT
Query on MLT

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth A],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A],
R [auth B],
S [auth B],
T [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.194α = 90
b = 134.194β = 90
c = 81.94γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2018-09-29 
  • Released Date: 2019-02-06 
  • Deposition Author(s): Lee, D., Kim, K.J.

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Structure summary