1A5Z

LACTATE DEHYDROGENASE FROM THERMOTOGA MARITIMA (TMLDH)

• PDB DOI: https://doi.org/10.2210/pdb1A5Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-02-18 Released: 1999-03-23 
• Deposition Author(s): Auerbach, G., Ostendorp, R., Prade, L., Korndoerfer, I., Dams, T., Huber, R., Jaenicke, R.

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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 

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

• PubMed: 9655830 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie Abt. Strukturforschung, 82152, Martinsried, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 36.8 kDa 
• Atom Count: 2,840 
• Modelled Residue Count: 312 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE	A	319	Thermotoga maritima	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	H [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
FBP	B [auth A], C [auth A]	1,6-di-O-phosphono-beta-D-fructofuranose C6 H14 O12 P2 RNBGYGVWRKECFJ-ARQDHWQXSA-N
CD	D [auth A], E [auth A], F [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
OXM	G [auth A]	OXAMIC ACID C2 H3 N O3 SOWBFZRMHSNYGE-UHFFFAOYSA-N

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 = 105.48	α = 90
b = 105.48	β = 90
c = 187.7	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Auerbach, G., Ostendorp, R., Prade, L., Korndoerfer, I., Dams, T., Huber, R., Jaenicke, R.

Revision History  

• 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