2IHU

Carboxyethylarginine synthase from Streptomyces clavuligerus: putative reaction intermediate complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic studies on N(2)-(2-carboxyethyl)arginine synthase.

Caines, M.E.Sorensen, J.L.Schofield, C.J.

(2009) Biochem.Biophys.Res.Commun. 385: 512-517

  • DOI: 10.1016/j.bbrc.2009.05.095
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N(2)-(2-Carboxyethyl)arginine synthase (CEAS), an unusual thiamin diphosphate (ThDP)-dependent enzyme, catalyses the committed step in the biosynthesis of the b-lactamase inhibitor clavulanic acid in Streptomyces clavuligerus. Crystal structures of t ...

    N(2)-(2-Carboxyethyl)arginine synthase (CEAS), an unusual thiamin diphosphate (ThDP)-dependent enzyme, catalyses the committed step in the biosynthesis of the b-lactamase inhibitor clavulanic acid in Streptomyces clavuligerus. Crystal structures of tetrameric CEAS-ThDP in complex with the substrate analogues 5-guanidinovaleric acid (GVA) and tartrate, and a structure reflecting a possible enol(ate)-ThDP reaction intermediate are described. The structures suggest overlapping binding sites for the substrates D-glyceraldehyde-3-phosphate (D-G3P) and L-arginine, and are consistent with the proposed CEAS mechanism in which D-G3P binds at the active site and reacts to form an alpha,beta-unsaturated intermediate,which subsequently undergoes (1,4)-Michael addition with the alpha-amino group of L-arginine. Additional solution studies are presented which probe the amino acid substrate tolerance of CEAS, providing further insight into the L-arginine binding site. These findings may facilitate the engineering of CEAS towards the synthesis of alternative beta-amino acid products.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX13TA, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxyethylarginine synthase
A, B, C, D
573Streptomyces clavuligerusMutation(s): 0 
Gene Names: ceaS
EC: 2.5.1.66
Find proteins for Q9LCV9 (Streptomyces clavuligerus)
Go to UniProtKB:  Q9LCV9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
TAR
Query on TAR

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Download CCD File 
A, D
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TP9
Query on TP9

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Download CCD File 
A, B, C, D
(3Z)-4-{[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]AMINO}-3-MERCAPTOPENT-3-EN-1-YL TRIHYDROGEN DIPHOSPHATE
C11 H18 N4 O7 P2 S
WTQDUFKDQLXDPH-YFHOEESVSA-L
 Ligand Interaction
TP8
Query on TP8

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Download CCD File 
C
5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-[(1Z)-1-HYDROXY-3-(PHOSPHONOOXY)PROP-1-EN-1-YL]-3-{[(4Z)-4-IMINO-2-METHYL-4,5-DIHYDROPYRIMIDIN-5-YL]METHYL}-4-METHYL-1,3-THIAZOL-3-IUM
PUTATIVE ENOL(ATE)-THDP REACTION INTERMEDIATE
C15 H21 N4 O12 P3 S
IYJJFPCOWJABBY-AOCMNYQTSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.691α = 90.00
b = 127.863β = 90.00
c = 197.150γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
REFMACphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance