9LDT

DESIGN AND SYNTHESIS OF NEW ENZYMES BASED ON THE LACTATE DEHYDROGENASE FRAMEWORK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design and synthesis of new enzymes based on the lactate dehydrogenase framework.

Dunn, C.R.Wilks, H.M.Halsall, D.J.Atkinson, T.Clarke, A.R.Muirhead, H.Holbrook, J.J.

(1991) Philos.Trans.R.Soc.London,Ser.B 332: 177-184

  • DOI: 10.1098/rstb.1991.0047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Analysis of the mechanism and structure of lactate dehydrogenases is summarized in a map of the catalytic pathway. Chemical probes, single tryptophan residues inserted at specific sites and a crystal structure reveal slow movements of the protein fra ...

    Analysis of the mechanism and structure of lactate dehydrogenases is summarized in a map of the catalytic pathway. Chemical probes, single tryptophan residues inserted at specific sites and a crystal structure reveal slow movements of the protein framework that discriminate between closely related small substrates. Only small and correctly charged substrates allow the protein to engulf the substrate in an internal vacuole that is isolated from solvent protons, in which water is frozen and hydride transfer is rapid. The closed vacuole is very sensitive to the size and charge of the substrate and provides discrimination between small substrates that otherwise have too few functional groups to be distinguished at a solvated protein surface. This model was tested against its ability to successfully predict the design and synthesis of new enzymes such as L-hydroxyisocaproate dehydrogenase and fully active malate dehydrogenase. Solvent friction limits the rate of forming the vacuole and thus the maximum rate of catalysis.


    Organizational Affiliation

    University of Bristol Molecular Recognition Centre, School of Medical Sciences, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LACTATE DEHYDROGENASE
A, B
332Sus scrofaMutation(s): 0 
Gene Names: LDHA
EC: 1.1.1.27
Find proteins for P00339 (Sus scrofa)
Go to Gene View: LDHA
Go to UniProtKB:  P00339
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXM
Query on OXM

Download SDF File 
Download CCD File 
A, B
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

--

External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OXMKi: 26000 - 138000 nM (92) BINDINGDB
OXMIC50: 57200 nM (92) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 60.300α = 90.00
b = 136.390β = 90.00
c = 86.050γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other