Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 86.51 kDa 
• Atom Count: 6257 
• Residue Count: 760 
• Unique protein chains: 1

1U08

Crystal Structure and Reactivity of YbdL from Escherichia coli Identify a Methionine Aminotransferase Function.

• DOI: 10.2210/pdb1U08/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-07-13 Released: 2004-07-27 
• Deposition Author(s): Dolzan, M., Johansson, K., Roig-Zamboni, V., Campanacci, V., Tegoni, M., Schneider, G., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Literature

Crystal structure and reactivity of YbdL from Escherichia coli identify a methionine aminotransferase function

Dolzan, M., Johansson, K., Roig-Zamboni, V., Campanacci, V., Tegoni, M., Schneider, G., Cambillau, C.

(2004) FEBS Lett 571: 141-146

• PubMed: 15280032 
• DOI: 10.1016/j.febslet.2004.06.075
• Primary Citation of Related Structures:  
  1U08


• PubMed Abstract: 
  

The ybdL gene of Escherichia coli codes for a protein of unknown function. Sequence analysis showed moderate homology to several vitamin B(6) dependent enzymes, suggesting that it may bind pyridoxal-5'-phosphate. The structure analysis of YbdL to 2.35 A resolution by protein crystallography verifies that it is a PLP dependent enzyme of fold type I, the typical aspartate aminotransferase fold. The active site contains a bound pyridoxal-5'-phosphate, covalently attached to the conserved active site lysine residue Lys236. The pattern of conserved amino acids in the putative substrate binding pocket of the enzyme reveals that it is most closely related to a hyperthermophilic aromatic residue aminotransferase from the archeon Pyrococcus horikoshii. Activity tests with 10 amino acids as amino-donors reveal, however, a preference for Met, followed by His and Phe, results which can be rationalized by modelization studies.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, UMR 6098, CNRS and Universités d'Aix-Marseille I and II, 31 chemin J. Aiguier, F-13402 Marseille Cedex 20, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical aminotransferase ybdL	A, B	386	Escherichia coli	Mutation(s): 0  Gene Names: ybdL EC: 2.6.1 (PDB Primary Data), 2.6.1.88 (UniProt)
Find proteins for P77806 (Escherichia coli (strain K12)) Explore P77806  Go to UniProtKB:  P77806

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.225 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.4	α = 90
b = 104.31	β = 90
c = 168.38	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-13 
• Released Date: 2004-07-27 
Deposition Author(s): Dolzan, M., Johansson, K., Roig-Zamboni, V., Campanacci, V., Tegoni, M., Schneider, G., Cambillau, C.

Revision History 

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance