3MQH

crystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with CoA and UDP-3-amino-2-acetamido-2,3-dideoxy glucuronic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted MJZClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Molecular structure of WlbB, a bacterial N-acetyltransferase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid .

Thoden, J.B.Holden, H.M.

(2010) Biochemistry 49: 4644-4653

  • DOI: https://doi.org/10.1021/bi1005738
  • Primary Citation of Related Structures:  
    3MQG, 3MQH

  • PubMed Abstract: 

    The pathogenic bacteria Pseudomonas aeruginosa and Bordetella pertussis contain in their outer membranes the rare sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid. Five enzymes are required for the biosynthesis of this sugar starting from UDP-N-acetylglucosamine. One of these, referred to as WlbB, is an N-acetyltransferase that converts UDP-2-acetamido-3-amino-2,3-dideoxy-d-glucuronic acid (UDP-GlcNAc3NA) to UDP-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid (UDP-GlcNAc3NAcA). Here we report the three-dimensional structure of WlbB from Bordetella petrii. For this analysis, two ternary structures were determined to 1.43 A resolution: one in which the protein was complexed with acetyl-CoA and UDP and the second in which the protein contained bound CoA and UDP-GlcNAc3NA. WlbB adopts a trimeric quaternary structure and belongs to the LbetaH superfamily of N-acyltransferases. Each subunit contains 27 beta-strands, 23 of which form the canonical left-handed beta-helix. There are only two hydrogen bonds that occur between the protein and the GlcNAc3NA moiety, one between O(delta1) of Asn 84 and the sugar C-3' amino group and the second between the backbone amide group of Arg 94 and the sugar C-5' carboxylate. The sugar C-3' amino group is ideally positioned in the active site to attack the si face of acetyl-CoA. Given that there are no protein side chains that can function as general bases within the GlcNAc3NA binding pocket, a reaction mechanism is proposed for WlbB whereby the sulfur of CoA ultimately functions as the proton acceptor required for catalysis.


  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharides biosynthesis acetyltransferase
A, B, C, D, E
192Bordetella petrii DSM 12804Mutation(s): 0 
Gene Names: Bpet4817wlbB
EC: 2.3.1
UniProt
Find proteins for A9IH93 (Bordetella petrii (strain ATCC BAA-461 / DSM 12804 / CCUG 43448))
Explore A9IH93 
Go to UniProtKB:  A9IH93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9IH93
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download Ideal Coordinates CCD File 
DA [auth E]
FA [auth F]
H [auth A]
M [auth B]
P [auth C]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
MJZ
Query on MJZ

Download Ideal Coordinates CCD File 
CA [auth E]
G [auth A]
GA [auth F]
L [auth B]
Q [auth C]
(2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid
C17 H26 N4 O17 P2
RRAQYLXLCYIZBB-HHKCBAECSA-N
PE4
Query on PE4

Download Ideal Coordinates CCD File 
V [auth C]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
HA [auth F],
R [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
I [auth A]
IA [auth F]
K [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.466α = 90
b = 107.891β = 102.55
c = 91.269γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted COAClick on this verticalbar to view detailsBest fitted MJZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description