1LDC

X-RAY STRUCTURE OF TWO COMPLEXES OF THE Y143F FLAVOCYTOCHROME B2 MUTANT CRYSTALLIZED IN THE PRESENCE OF LACTATE OR PHENYL-LACTATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

X-ray structure of two complexes of the Y143F flavocytochrome b2 mutant crystallized in the presence of lactate or phenyl lactate.

Tegoni, M.Begotti, S.Cambillau, C.

(1995) Biochemistry 34: 9840-9850

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavocytochrome b2 is a flavohemo enzyme localized in the intermembrane space of yeast mitochondria, where it catalyzes the electron transfer from its substrate, L-lactate, to cytochrome c. We have obtained crystals of a flavocytochrome b2 mutant, Y1 ...

    Flavocytochrome b2 is a flavohemo enzyme localized in the intermembrane space of yeast mitochondria, where it catalyzes the electron transfer from its substrate, L-lactate, to cytochrome c. We have obtained crystals of a flavocytochrome b2 mutant, Y143F, which are isostructural with those of the native recombinant enzyme [Tegoni, M., & Cambillau, C. (1994) Protein Sci.3, 303-314]. These crystals were grown under similar conditions to those used to obtain the recombinant enzyme, but in the presence of phenyl lactate or lactate. We report here on the structural analysis of the two complexes of flavocytochrome b2 with the reaction products at 2.9 A resolution. In both structures, the Phe143 phenyl ring keeps the same position as that of the phenolic ring of Tyr143 in both the native recombinant and in the native wild-type enzymes. The product of the reaction, phenyl pyruvate or pyruvate, is present at the active site of both subunits, and not only in subunit 2 as observed in the wild-type structure [Xia, Z.-X., & Mathews, F.S. (1990) J. Mol. Biol. 212, 837-863]. The number of interactions between the FMN and the heme domain is considerably lower in the Y143F mutant than in the native proteins. The latter finding strongly supports the hypothesis that the main role of Tyr143 in the native proteins. The latter findings strongly supports the hypothesis that the main role of Tyr143 in the native protein probably consists in establishing a hydrogen bond with the heme [Xia, Z.-X., & Mathews, F.S. (1990) J. Mol. Biol. 212, 837-863]. This interaction appears to be essential for the two domains to approach each other suitably so that the intramolecular electron transfer can occur.


    Organizational Affiliation

    Laboratoire de Cristallographie et Cristallisation des Macromolécules Biologiques, URA-1296 CNRS, Marseille, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-LACTATE DEHYDROGENASE
A, B
511Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: CYB2
EC: 1.1.2.3
Find proteins for P00175 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P00175
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYR
Query on PYR

Download SDF File 
Download CCD File 
A, B
PYRUVIC ACID
C3 H4 O3
LCTONWCANYUPML-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 164.500α = 90.00
b = 164.500β = 90.00
c = 114.000γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2012-06-27
    Type: Other, Structure summary