1A5Z

LACTATE DEHYDROGENASE FROM THERMOTOGA MARITIMA (TMLDH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Lactate dehydrogenase from the hyperthermophilic bacterium thermotoga maritima: the crystal structure at 2.1 A resolution reveals strategies for intrinsic protein stabilization.

Auerbach, G.Ostendorp, R.Prade, L.Korndorfer, I.Dams, T.Huber, R.Jaenicke, R.

(1998) Structure 6: 769-781

  • DOI: 10.1016/s0969-2126(98)00078-1
  • Primary Citation of Related Structures:  
    1A5Z

  • PubMed Abstract: 
  • L(+)-Lactate dehydrogenase (LDH) catalyzes the last step in anaerobic glycolysis, the conversion of pyruvate to lactate, with the concomitant oxidation of NADH. Extensive physicochemical and structural investigations of LDHs from both mesophilic and thermophilic organisms have been undertaken in order to study the temperature adaptation of proteins ...

    L(+)-Lactate dehydrogenase (LDH) catalyzes the last step in anaerobic glycolysis, the conversion of pyruvate to lactate, with the concomitant oxidation of NADH. Extensive physicochemical and structural investigations of LDHs from both mesophilic and thermophilic organisms have been undertaken in order to study the temperature adaptation of proteins. In this study we aimed to determine the high-resolution structure of LDH from the hyperthermophilic bacterium Thermotoga maritima (TmLDH), the most thermostable LDH to be isolated so far. It was hoped that the structure of TmLDH would serve as a model system to reveal strategies of protein stabilization at temperatures near the boiling point of water.


    Related Citations: 
    • Extremely Thermostable L(+)-Lactate Dehydrogenase from Thermotoga Maritima: Cloning, Characterization, and Crystallization of the Recombinant Enzyme in its Tetrameric and Octameric State
      Ostendorp, R., Auerbach, G., Jaenicke, R.
      (1996) Protein Sci 5: 862

    Organizational Affiliation

    Max-Planck-Institut für Biochemie Abt. Strukturforschung, 82152, Martinsried, Germany. auerbach@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-LACTATE DEHYDROGENASEA319Thermotoga maritimaMutation(s): 0 
EC: 1.1.1.27
UniProt
Find proteins for P16115 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P16115 
Go to UniProtKB:  P16115
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
H [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
FBP
Query on FBP

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
OXM
Query on OXM

Download Ideal Coordinates CCD File 
G [auth A]OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.48α = 90
b = 105.48β = 90
c = 187.7γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary