4CJ8 | pdb_00004cj8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.249 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 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 Biological Chem 289: 8041

  • DOI: https://doi.org/10.1074/jbc.M113.545384
  • Primary Citation 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 
  • Modeled Residue Count: 3,852 
  • Deposited Residue Count: 3,968 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOSYLTRANSFERASE FAMILY 6
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
248Bacteroides ovatusMutation(s): 1 
EC: 2.4.1.40

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UD2

Query on UD2


Download:Ideal Coordinates CCD File
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
UDP

Query on UDP


Download:Ideal Coordinates CCD File
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
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
U [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
NGA

Query on NGA


Download:Ideal Coordinates CCD File
SA [auth M],
UA [auth N]		2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
A2G

Query on A2G


Download:Ideal Coordinates CCD File
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
SO4

Query on SO4


Download:Ideal Coordinates CCD File
X [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
CA [auth D],
GA [auth G],
HA [auth G],
Q [auth A],
T [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.249 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.237 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.69α = 90
b = 79.74β = 95.23
c = 179.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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
  • Version 2.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary