4CJ8

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

PDB DOI: https://doi.org/10.2210/pdb4CJ8/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: 3.50 Å
R-Value Free: 0.249
R-Value Work: 0.225
R-Value Observed: 0.227

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: 478.89 kDa
Atom Count: 32,877
Modelled Residue Count: 3,852
Deposited Residue Count: 3,968
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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	248	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UD2 Query on UD2 Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth F] SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain VA [auth O] SDF format, chain WA [auth P] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain VA [auth O] MOL2 format, chain WA [auth P]	DA [auth E] EA [auth F] FA [auth G] IA [auth H] VA [auth O] DA [auth E], EA [auth F], FA [auth G], IA [auth H], VA [auth O], WA [auth P]	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE C₁₇ H₂₇ N₃ O₁₇ P₂ LFTYTUAZOPRMMI-NESSUJCYSA-N		Interactions Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain VA [auth O] Focus chain WA [auth P] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain VA [auth O] Focus chain WA [auth P]
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain JA [auth I] SDF format, chain LA [auth J] SDF format, chain NA [auth K] SDF format, chain PA [auth L] SDF format, chain R [auth A] SDF format, chain RA [auth M] SDF format, chain TA [auth N] SDF format, chain V [auth B] SDF format, chain Y [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain NA [auth K] MOL2 format, chain PA [auth L] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth M] MOL2 format, chain TA [auth N] MOL2 format, chain V [auth B] MOL2 format, chain Y [auth C]	AA [auth D] JA [auth I] LA [auth J] NA [auth K] PA [auth L] AA [auth D], JA [auth I], LA [auth J], NA [auth K], PA [auth L], R [auth A], RA [auth M], TA [auth N], V [auth B], Y [auth C]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain AA [auth D] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain PA [auth L] Focus chain R [auth A] Focus chain RA [auth M] Focus chain TA [auth N] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain JA [auth I] Focus chain LA [auth J] Focus chain NA [auth K] Focus chain PA [auth L] Focus chain R [auth A] Focus chain RA [auth M] Focus chain TA [auth N] Focus chain V [auth B] Focus chain Y [auth C]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A]	U [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
NGA Query on NGA Download Ideal Coordinates CCD File SDF format, chain SA [auth M] SDF format, chain UA [auth N] MOL2 format, chain SA [auth M] MOL2 format, chain UA [auth N]	SA [auth M], UA [auth N]	2-acetamido-2-deoxy-beta-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-JAJWTYFOSA-N		Interactions Focus chain SA [auth M] Focus chain UA [auth N] Interactions & Density Focus chain SA [auth M] Focus chain UA [auth N]
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain KA [auth I] SDF format, chain MA [auth J] SDF format, chain OA [auth K] SDF format, chain QA [auth L] SDF format, chain S [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain KA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain OA [auth K] MOL2 format, chain QA [auth L] MOL2 format, chain S [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth C]	BA [auth D] KA [auth I] MA [auth J] OA [auth K] QA [auth L] BA [auth D], KA [auth I], MA [auth J], OA [auth K], QA [auth L], S [auth A], W [auth B], Z [auth C]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain BA [auth D] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain S [auth A] Focus chain W [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain KA [auth I] Focus chain MA [auth J] Focus chain OA [auth K] Focus chain QA [auth L] Focus chain S [auth A] Focus chain W [auth B] Focus chain Z [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B]	X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain Q [auth A] SDF format, chain T [auth A] MOL2 format, chain CA [auth D] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth A]	CA [auth D], GA [auth G], HA [auth G], Q [auth A], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain Q [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth D] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain Q [auth A] Focus chain T [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.249
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.69	α = 90
b = 79.74	β = 95.23
c = 179.08	γ = 90

Software Package:

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

Structure Validation

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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

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Help and Resources

4CJ8

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)