2IHU | pdb_00002ihu

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 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2IHU

This is version 1.2 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: https://doi.org/10.1016/j.bbrc.2009.05.095
  • Primary Citation Related Structures: 
    2IHT, 2IHU, 2IHV

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 246.81 kDa 
  • Atom Count: 18,287 
  • Modeled Residue Count: 2,216 
  • Deposited Residue Count: 2,292 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carboxyethylarginine synthase
A, B, C, D
573Streptomyces clavuligerusMutation(s): 0 
Gene Names: ceas2
EC: 2.5.1.66
UniProt
Find proteins for Q9LCV9 (Streptomyces clavuligerus)
Explore Q9LCV9 
Go to UniProtKB:  Q9LCV9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LCV9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TP8

Query on TP8



Download:Ideal Coordinates CCD File
Q [auth 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
C15 H21 N4 O12 P3 S
IYJJFPCOWJABBY-AOCMNYQTSA-L
TP9

Query on TP9



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
R [auth C],
U [auth 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
TAR

Query on TAR



Download:Ideal Coordinates CCD File
I [auth A],
V [auth D]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
M [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
K [auth B]
O [auth C]
P [auth C]
F [auth A],
G [auth A],
K [auth B],
O [auth C],
P [auth C],
T [auth D]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B],
N [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.201 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.691α = 90
b = 127.863β = 90
c = 197.15γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary