2WGZ | pdb_00002wgz

Crystal structure of alpha-1,3 galactosyltransferase (alpha3GT) in a complex with p-nitrophenyl-beta-galactoside (pNP-beta-Gal)

PDB DOI: https://doi.org/10.2210/pdb2WGZ/pdb

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

Deposited: 2009-04-28 Released: 2009-06-16
Deposition Author(s): Jamaluddin, H., Tumbale, P., Ferns, T.A., Thiyagarajan, N., Brew, K., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free:
0.206 (Depositor)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of Alpha-1,3 Galactosyltransferase (Alpha3Gt) in a Complex with P-Nitrophenyl-Beta-Galactoside (Pnpbetagal).

Jamaluddin, H., Tumbale, P., Ferns, T.A., Thiyagarajan, N., Brew, K., Acharya, K.R.

(2009) Biochem Biophys Res Commun 385: 601

PubMed: 19486884 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2009.05.111
Primary Citation Related Structures:
2WGZ

PubMed Abstract:
The specificities of glycosyltransferases make them useful for the synthesis of biologically active oligosaccharides, but also restrict their range of products. In substrate engineering, substrate promiscuity is enhanced by attaching removable interactive groups to weak substrates. Thus, the attachment of betap-nitrophenyl converts galactose from a poor into a good substrate of alpha-1,3-galactosyltransferase. The crystallographic structure of a complex of alpha3GT containing p-nitrophenyl-beta-galactoside shows that the p-nitrophenyl binds similarly to the N-acetylglucosamine of the substrate, N-acetyllactosamine, interacting with the indole of Trp249. p-Nitrophenyl, unlike N-acetylglucosamine, makes no H-bonds but has more non-polar interactions, making it an effective monosaccharide mimetic.

Organizational Affiliation

Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA27AY, UK.

Macromolecule Content

Total Structure Weight: 70.59 kDa
Atom Count: 5,487
Modeled Residue Count: 574
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYL TRANSFERASE	A, B	290	Bos taurus	Mutation(s): 0 EC: 2.4.1.151 (PDB Primary Data), 2.4.1.87 (PDB Primary Data)
UniProt
Find proteins for P14769 (Bos taurus) Explore P14769 Go to UniProtKB: P14769
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
147 Query on 147 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-nitrophenyl beta-D-galactopyranoside C₁₂ H₁₅ N O₈ IFBHRQDFSNCLOZ-YBXAARCKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GAL Query on GAL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
NPO Query on NPO 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]	P-NITROPHENOL C₆ H₅ N O₃ BTJIUGUIPKRLHP-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] I [auth A] N [auth B] F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain L [auth B]	D [auth A], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.12 Å
R-Value Free: 0.206 (Depositor)
R-Value Work: 0.169 (Depositor), 0.169 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.146	α = 90
b = 94.222	β = 99.05
c = 94.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-06-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary