1GVG

Crystal Structure of Clavaminate Synthase with Nitric Oxide

• PDB DOI: https://doi.org/10.2210/pdb1GVG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces clavuligerus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-02-12 Released: 2003-02-07 
• Deposition Author(s): Zhang, Z.H., Ren, J., McKinnon, C.H., Clifton, I.J., Harlos, K., Schofield, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.204 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Crystal Structure of a Clavaminate Synthase-Fe(II) -2-Oxoglutarate-Substrate-No Complex: Evidence for Metal Centered Rearrangements

Zhang, Z.H., Ren, J., Harlos, K., McKinnon, C.H., Clifton, I.J., Schofield, C.J.

(2002) FEBS Lett 517: 7

• PubMed: 12062399 
• DOI: https://doi.org/10.1016/s0014-5793(02)02520-6
• Primary Citation of Related Structures:  
  1GVG


• PubMed Abstract: 
  

  Clavaminate synthase (CAS), a 2-oxoglutarate (2OG) dependent dioxygenase, catalyses three steps in the biosynthesis of clavulanic acid. Crystals of CAS complexed with Fe(II), 2OG and deoxyguanidinoproclavaminate were exposed to nitric oxide (NO) acting as a dioxygen analogue. Prior to exposure with NO, the active site Fe(II) is octahedrally coordinated by a water molecule, the 2-oxo and 1-carboxylate groups of 2OG, and the side-chains of an aspartyl and two histidinyl residues. NO binds to the position previously occupied by the 2OG 1-carboxylate concomitant with rearrangement of the latter to the position previously occupied by the displaced water.

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Organizational Affiliation: 

The Oxford Centre for Molecular Sciences and The Dyson Perrins Laboratory, The Department of Chemistry, South Parks Road, Oxford, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 36.17 kDa 
• Atom Count: 2,870 
• Modelled Residue Count: 315 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLAVAMINATE SYNTHASE 1	A	324	Streptomyces clavuligerus	Mutation(s): 0  EC: 1.14.11.21
UniProt
Find proteins for Q05581 (Streptomyces clavuligerus) Explore Q05581  Go to UniProtKB:  Q05581

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCX	G [auth A]	DEOXYGUANIDINOPROCLAVAMINIC ACID C9 H16 N4 O3 UYADDEKIZFRINK-LURJTMIESA-N
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
HOA	H [auth A]	HYDROXYAMINE H3 N O AVXURJPOCDRRFD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.204 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.27	α = 90
b = 69.52	β = 90
c = 70.19	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-07 
Deposition Author(s): Zhang, Z.H., Ren, J., McKinnon, C.H., Clifton, I.J., Harlos, K., Schofield, C.J.

Revision History  

• Version 1.0: 2003-02-07
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-07-05
  Changes: Refinement description
• Version 1.4: 2018-05-23
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description