Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 149.39 kDa 
• Atom Count: 10312 
• Modelled Residue Count: 1272 
• Deposited Residue Count: 1308 
• Unique protein chains: 1

1L5A

Crystal Structure of VibH, an NRPS Condensation Enzyme

• PDB DOI: 10.2210/pdb1L5A/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Vibrio cholerae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-03-06 Released: 2002-06-26 
• Deposition Author(s): Keating, T.A., Marshall, C.G., Walsh, C.T., Keating, A.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.259 

Literature

The structure of VibH represents nonribosomal peptide synthetase condensation, cyclization and epimerization domains.

Keating, T.A., Marshall, C.G., Walsh, C.T., Keating, A.E.

(2002) Nat Struct Biol 9: 522-526

• PubMed: 12055621 
• DOI: 10.1038/nsb810
• Primary Citation of Related Structures:  
  1L5A


• PubMed Abstract: 
  

Nonribosomal peptide synthetases (NRPSs) are large, multidomain enzymes that biosynthesize medically important natural products. We report the crystal structure of the free-standing NRPS condensation (C) domain VibH, which catalyzes amide bond formation in the synthesis of vibriobactin, a Vibrio cholerae siderophore. Despite low sequence identity, NRPS condensation enzymes are structurally related to chloramphenicol acetyltransferase (CAT) and dihydrolipoamide acyltransferases. However, although the latter enzymes are homotrimers, VibH is a monomeric pseudodimer. The VibH structure is representative of both NRPS condensation and epimerization domains, as well as the condensation-variant cyclization domains, which are all expected to be monomers. Surprisingly, despite favorable positioning in the active site, a universally conserved histidine important in CAT and in other C domains is not critical for general base catalysis in VibH.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
amide synthase	A, B, C	436	Vibrio cholerae	Mutation(s): 0  Gene Names: vibH
UniProt
Find proteins for Q9KTV9 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KTV9  Go to UniProtKB:  Q9KTV9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.259 
• R-Value Work: 0.214 
• R-Value Observed: 0.259 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.595	α = 90
b = 161.349	β = 104.81
c = 115.602	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-06 
• Released Date: 2002-06-26 
Deposition Author(s): Keating, T.A., Marshall, C.G., Walsh, C.T., Keating, A.E.

Revision History  

• Version 1.0: 2002-06-26
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance