2IHV | pdb_00002ihv

Carboxyethylarginine synthase from Streptomyces clavuligerus: 5-guanidinovaleric acid complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.161 (Depositor) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: 246.53 kDa 
  • Atom Count: 18,002 
  • Modeled Residue Count: 2,240 
  • 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP

Query on TPP



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
Q [auth C],
U [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
GVA

Query on GVA



Download:Ideal Coordinates CCD File
H [auth A],
M [auth B],
R [auth C],
V [auth D]
5-{[AMINO(IMINO)METHYL]AMINO}PENTANOIC ACID
C6 H13 N3 O2
UKUBCVAQGIZRHL-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A]
J [auth B]
K [auth B]
O [auth C]
P [auth C]
F [auth A],
J [auth B],
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],
I [auth B],
N [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.161 (Depositor) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.744α = 90
b = 128.297β = 90
c = 197.638γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description