1YRO | pdb_00001yro

Crystal structure of beta14,-galactosyltransferase mutant ARG228Lys in complex with alpha-lactalbumin in the presence of UDP-galactose and Mn

PDB DOI: https://doi.org/10.2210/pdb1YRO/pdb

Classification: TRANSFERASE ACTIVATOR/TRANSFERASE
Organism(s): Mus musculus, Bos taurus
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2005-02-04 Released: 2005-03-22
Deposition Author(s): Ramakrishnan, B., Boeggeman, E., Qasba, P.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.225 (Depositor), 0.221 (DCC)
R-Value Work:
0.189 (Depositor), 0.185 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Mutation of Arginine 228 to Lysine Enhances the Glucosyltransferase Activity of Bovine beta-1,4-Galactosyltransferase I

Ramakrishnan, B., Boeggeman, E., Qasba, P.K.

(2005) Biochemistry 44: 3202-3210

PubMed: 15736931 Search on PubMed
DOI: https://doi.org/10.1021/bi0479454
Primary Citation Related Structures:
1YRO

PubMed Abstract:
Beta-1,4-galactosyltransferase I (beta4Gal-T1) normally transfers Gal from UDP-Gal to GlcNAc in the presence of Mn(2+) ion (Gal-T activity) and also transfers Glc from UDP-Glc to GlcNAc (Glc-T activity), albeit at only 0.3% efficiency. In addition, alpha-lactalbumin (LA) enhances this Glc-T activity more than 25 times. Comparison of the crystal structures of UDP-Gal- and UDP-Glc-bound beta4Gal-T1 reveals that the O4 hydroxyl group in both Gal and Glc moieties forms a hydrogen bond with the side chain carboxylate group of Glu317. The orientation of the O4 hydroxyl of glucose causes a steric hindrance to the side chain carboxylate group of Glu317, accounting for the enzyme's low Glc-T activity. In this study, we show that mutation of Arg228, a residue in the vicinity of Glu317, to lysine (R228K-Gal-T1) results in a 15-fold higher Glc-T activity, which is further enhanced by LA to nearly 25% of the Gal-T activity of the wild type. The kinetic parameters indicate that the main effect of the mutation of Arg228 to lysine is on the k(cat) of Glc-T, which increases 3-4-fold, both in the absence and in the presence of LA; simultaneously, the k(cat) for the Gal-T reaction is reduced 30-fold. The crystal structure of R228K-Gal-T1 complexed with LA, UDP-Gal, and Mn(2+) determined at 1.9 A resolution shows that the Asp318 side chain exhibits a minor alternate conformation, compared to that in the wild type. This alternate conformation now causes a steric hindrance to the O4 hydroxyl group of the Gal moiety of UDP-Gal, probably causing the dissociation of UDP-Gal and the reduced k(cat) of the Gal-T reaction.

Organizational Affiliation

Structural Glycobiology Section, Laboratory of Experimental and Computational Biology, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland 21702-1201, USA.

Macromolecule Content

Total Structure Weight: 96.39 kDa
Atom Count: 7,388
Modeled Residue Count: 790
Deposited Residue Count: 818
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-LACTALBUMIN	A, C	123	Mus musculus	Mutation(s): 0 Gene Names: alpha-lactalbumin
UniProt
Find proteins for P29752 (Mus musculus) Explore P29752 Go to UniProtKB: P29752
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29752
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-1,4-GALACTOSYLTRANSFERASE	B, D	286	Bos taurus	Mutation(s): 2 Gene Names: beta1, 4-galactosyltransferase EC: 2.4.1.22 (PDB Primary Data), 2.4.1.90 (PDB Primary Data), 2.4.1.38 (PDB Primary Data), 2.4.1 (UniProt), 2.4.1.275 (UniProt)
UniProt
Find proteins for P08037 (Bos taurus) Explore P08037 Go to UniProtKB: P08037
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08037
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDU Query on GDU Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D] mmCIF format, chain H [auth B] mmCIF format, chain M [auth D]	H [auth B], M [auth D]	GALACTOSE-URIDINE-5'-DIPHOSPHATE C₁₅ H₂₄ N₂ O₁₇ P₂ HSCJRCZFDFQWRP-ABVWGUQPSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D] Interactions & Density Focus chain H [auth B] Focus chain M [auth D]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B]	J [auth B], O [auth D]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain J [auth B] Focus chain O [auth D] Interactions & Density Focus chain J [auth B] Focus chain O [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain L [auth C]	G [auth A], L [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain L [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D] mmCIF format, chain I [auth B] mmCIF format, chain N [auth D]	I [auth B], N [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C]	E [auth A], K [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth C]