2OI7

E. coli GlmU- Complex with UDP-GlcNAc, desulpho-CoA and GlcNAc-1-PO4

PDB DOI: https://doi.org/10.2210/pdb2OI7/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-01-10 Released: 2007-06-19
Deposition Author(s): Olsen, L.R., Vetting, M.W., Roderick, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.247
R-Value Work: 0.209
R-Value Observed: 0.209

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of the E. coli bifunctional GlmU acetyltransferase active site with substrates and products.

Olsen, L.R., Vetting, M.W., Roderick, S.L.

(2007) Protein Sci 16: 1230-1235

PubMed: 17473010 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1110/ps.072779707
Primary Citation of Related Structures:
2OI5, 2OI6, 2OI7

PubMed Abstract:
The biosynthesis of UDP-GlcNAc in bacteria is carried out by GlmU, an essential bifunctional uridyltransferase that catalyzes the CoA-dependent acetylation of GlcN-1-PO(4) to form GlcNAc-1-PO(4) and its subsequent condensation with UTP to form pyrophosphate and UDP-GlcNAc. As a metabolite, UDP-GlcNAc is situated at a branch point leading to the biosynthesis of lipopolysaccharide and peptidoglycan. Consequently, GlmU is regarded as an important target for potential antibacterial agents. The crystal structure of the Escherichia coli GlmU acetyltransferase active site has been determined in complexes with acetyl-CoA, CoA/GlcN-1-PO(4), and desulpho-CoA/GlcNAc-1-PO(4). These structures reveal the enzyme groups responsible for binding the substrates. A superposition of these complex structures suggests that the 2-amino group of GlcN-1-PO(4) is positioned in proximity to the acetyl-CoA to facilitate direct attack on its thioester by a ternary complex mechanism.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

Macromolecule Content

Total Structure Weight: 102.09 kDa
Atom Count: 7,160
Modelled Residue Count: 899
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein glmU	A, B	456	Escherichia coli	Mutation(s): 0 Gene Names: glmU EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
UniProt
Find proteins for P0ACC7 (Escherichia coli (strain K12)) Explore P0ACC7 Go to UniProtKB: P0ACC7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ACC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCA Query on DCA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	DESULFO-COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ ILWZMFJBPIYQKW-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
UD1 Query on UD1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-CFRASDGPSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
GN1 Query on GN1 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C₈ H₁₆ N O₉ P FZLJPEPAYPUMMR-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	D [auth A], I [auth B], J [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.247
R-Value Work: 0.209
R-Value Observed: 0.209
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.969	α = 90
b = 102.969	β = 90
c = 644.076	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CTR	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Olsen, L.R.

Vetting, M.W.

Roderick, S.L.

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary