4CJC

orthorhombic crystal form of Bogt6a E192Q in complex with UDP-GalNAc, UDP, GalNAc

PDB DOI: https://doi.org/10.2210/pdb4CJC/pdb

Classification: TRANSFERASE
Organism(s): Bacteroides ovatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-12-19 Released: 2014-02-05
Deposition Author(s): Pham, T., Stinson, B., Thiyagarajan, N., Lizotte-Waniewski, M., Brew, K., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.42 Å
R-Value Free: 0.314
R-Value Work: 0.283
R-Value Observed: 0.285

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of Complexes of a Metal-Independent Glycosyltransferase Gt6 from Bacteroides Ovatus with Udp-Galnac and its Hydrolysis Products.

Pham, T.T.K., Stinson, B., Thiyagarajan, N., Lizotte-Waniewski, M., Brew, K., Acharya, K.R.

(2014) J Biol Chem 289: 8041

PubMed: 24459149 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.545384
Primary Citation of Related Structures:
4CJ8, 4CJB, 4CJC

PubMed Abstract:
Mammalian members of glycosyltransferase family 6 (GT6) of the CAZy database have a GT-A fold containing a conserved Asp-X-Asp (DXD) sequence that binds an essential metal cofactor. Bacteroides ovatus GT6a represents a GT6 clade found in more than 30 Gram-negative bacteria that is similar in sequence to the catalytic domains of mammalian GT6, but has an Asn(95)-Ala-Asn(97) (NXN) sequence substituted for the DXD motif and metal-independent catalytic activity. Co-crystals of a low activity mutant of BoGT6a (E192Q) with UDP-GalNAc contained protein complexes with intact UDP-GalNAc and two forms with hydrolysis products (UDP plus GalNAc) representing an initial closed complex and later open form primed for product release. Two cationic residues near the C terminus of BoGT6a, Lys(231) and Arg(243), interact with the diphosphate moiety of UDP-GalNAc, but only Lys(231) interacts with the UDP product and may function in leaving group stabilization. The amide group of Asn(95), the first Asn of the NXN motif, interacts with the ribose moiety of the substrate. This metal-independent GT6 resembles its metal-dependent homologs in undergoing conformational changes on binding UDP-GalNAc that arise from structuring the C terminus to cover this substrate. It appears that in the GT6 family, the metal cofactor functions specifically in binding the UDP moiety in the donor substrate and transition state, actions that can be efficiently performed by components of the polypeptide chain.

Organizational Affiliation

From the Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom and.

Macromolecule Content

Total Structure Weight: 118.61 kDa
Atom Count: 8,120
Modelled Residue Count: 955
Deposited Residue Count: 984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOSYLTRANSFERASE FAMILY 6	A, B, C, D	246	Bacteroides ovatus	Mutation(s): 1 EC: 2.4.1.40
UniProt
Find proteins for A7LVT2 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153)) Explore A7LVT2 Go to UniProtKB: A7LVT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7LVT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD2 Query on UD2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C]	E [auth A], H [auth C]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-NESSUJCYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D]	F [auth B], I [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D]	G [auth B], J [auth D]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.42 Å
R-Value Free: 0.314
R-Value Work: 0.283
R-Value Observed: 0.285
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.12	α = 90
b = 120.15	β = 90
c = 131.83	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-05

Deposition Author(s):

Pham, T.

Stinson, B.

Thiyagarajan, N.

Lizotte-Waniewski, M.

Brew, K.

Acharya, K.R.

Revision History (Full details and data files)

Version 1.0: 2014-02-05
Type: Initial release
Version 1.1: 2014-04-02
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary