4OXI

Crystal structure of Vibrio cholerae adenylation domain AlmE in complex with glycyl-adenosine-5'-phosphate

• PDB DOI:  https://doi.org/10.2210/pdb4OXI/pdb

• Classification: LIGASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-02-05 Released: 2014-12-31 
• Deposition Author(s): Fage, C.D., Henderson, J.C., Keatinge-Clay, A.T., Trent, M.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Army Research Office

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.193 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Antimicrobial peptide resistance of Vibrio cholerae results from an LPS modification pathway related to nonribosomal peptide synthetases.

Henderson, J.C., Fage, C.D., Cannon, J.R., Brodbelt, J.S., Keatinge-Clay, A.T., Trent, M.S.

(2014) ACS Chem Biol 9: 2382-2392

• PubMed: 25068415 
• DOI: https://doi.org/10.1021/cb500438x
• Primary Citation of Related Structures:  
  4OXI


• PubMed Abstract: 
  

The current pandemic El Tor biotype of O1 Vibrio cholerae is resistant to polymyxins, whereas the previous pandemic strain of the classical biotype is polymyxin sensitive. The almEFG operon found in El Tor V. cholerae confers >100-fold resistance to polymyxins through the glycylation of lipopolysaccharide. Here, we present the mechanistic determination of initial steps in the AlmEFG pathway. We verify that AlmF is an aminoacyl carrier protein and identify AlmE as the enzyme required to activate AlmF as a functional carrier protein. A combination of structural information and activity assays was used to identify a pair of active site residues that are important for mediating AlmE glycine specificity. Overall, the structure of AlmE in complex with its glycyl-adenylate intermediate reveals that AlmE is related to Gram-positive d-alanine/d-alanyl carrier protein ligase, while the trio of proteins in the AlmEFG system forms a chemical pathway that resembles the division of labor in nonribosomal peptide synthetases.

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Organizational Affiliation: 

Department of Molecular Biosciences, ‡Department of Chemistry, §Institute of Cellular and Molecular Biology, The University of Texas at Austin , Austin, Texas 78712, United States.

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: 65.77 kDa 
• Atom Count: 4,398 
• Modelled Residue Count: 526 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterobactin synthetase component F-related protein	A	576	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0  Gene Names: VC_1579
UniProt
Find proteins for Q9KRQ7 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KRQ7  Go to UniProtKB:  Q9KRQ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GAP	B [auth A]	GLYCYL-ADENOSINE-5'-PHOSPHATE C12 H17 N6 O8 P HROXHMRQKGGIFT-JJNLEZRASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.193 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.039	α = 90
b = 116.039	β = 90
c = 99.584	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Fage, C.D., Henderson, J.C., Keatinge-Clay, A.T., Trent, M.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106112
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI064184
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI76322
Army Research Office	United States	W911NF-12-1-0390

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-02-04
  Changes: Derived calculations
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description