Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 63.31 kDa 
• Atom Count: 4759 
• Modelled Residue Count: 559 
• Deposited Residue Count: 571 
• Unique protein chains: 2

2WOK

Clavulanic acid biosynthesis oligopeptide binding protein 2 complexed with bradykinin

• DOI: 10.2210/pdb2WOK/pdb

• Classification: PEPTIDE BINDING PROTEIN/PEPTIDE
• Organism(s): Streptomyces clavuligerus, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-26 Released: 2009-12-08 
• Deposition Author(s): Mackenzie, A.K., Valegard, K., Iqbal, A., Caines, M.E.C., Kershaw, N.J., Jensen, S.E., Schofield, C.J., Andersson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.

Mackenzie, A.K., Valegard, K., Iqbal, A., Caines, M.E., Kershaw, N.J., Jensen, S.E., Schofield, C.J., Andersson, I.

(2010) J Mol Biol 396: 332-344

• PubMed: 19941870 
• DOI: 10.1016/j.jmb.2009.11.045
• Primary Citation of Related Structures:  
  2WOP, 2WOK, 2WOL


• PubMed Abstract: 
  

Clavulanic acid (CA) is a clinically important beta-lactamase inhibitor that is produced by fermentation of Streptomyces clavuligerus. The CA biosynthesis pathway starts from arginine and glyceraldehyde-3-phosphate and proceeds via (3S,5S)-clavaminic acid, which is converted to (3R,5R)-clavaldehyde, the immediate precursor of (3R,5R)-CA. Open reading frames 7 (orf7) and 15 (orf15) of the CA biosynthesis cluster encode oligopeptide-binding proteins (OppA1 and OppA2), which are essential for CA biosynthesis. OppA1/2 are proposed to be involved in the binding and/or transport of peptides across the S. clavuligerus cell membrane. Peptide binding assays reveal that recombinant OppA1 and OppA2 bind di-/tripeptides containing arginine and certain nonapeptides including bradykinin. Crystal structures of OppA2 in its apo form and in complex with arginine or bradykinin were solved to 1.45, 1.7, and 1.7 A resolution, respectively. The overall fold of OppA2 consists of two lobes with a deep cavity in the center, as observed for other oligopeptide-binding proteins. The large cavity creates a peptide/arginine binding cleft. The crystal structures of OppA2 in complex with arginine or bradykinin reveal that the C-terminal arginine of bradykinin binds similarly to arginine. The results are discussed in terms of the possible roles of OppA1/2 in CA biosynthesis.

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Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLAVULANIC ACID BIOSYNTHESIS OLIGOPEPTIDE BINDING PROTEIN 2	A	562	Streptomyces clavuligerus	Mutation(s): 0  Gene Names: oppA2, SCLAV_4183
UniProt
Find proteins for Q8KRB4 (Streptomyces clavuligerus) Explore Q8KRB4  Go to UniProtKB:  Q8KRB4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kininogen-1	B	9	Homo sapiens	Mutation(s): 0  Gene Names: KNG1, BDK, KNG
UniProt & NIH Common Fund Data Resources
Find proteins for P01042 (Homo sapiens) Explore P01042  Go to UniProtKB:  P01042
PHAROS:  P01042 GTEx:  ENSG00000113889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.223 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.511	α = 90
b = 83.327	β = 95.54
c = 62.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-26 
• Released Date: 2009-12-08 
Deposition Author(s): Mackenzie, A.K., Valegard, K., Iqbal, A., Caines, M.E.C., Kershaw, N.J., Jensen, S.E., Schofield, C.J., Andersson, I.

Revision History  

• Version 1.0: 2009-12-08
  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: 2018-12-12
  Changes: Data collection, Database references, Source and taxonomy, Structure summary