2AH9 | pdb_00002ah9

Crystal Structure of Human M340H-Beta-1,4-Galactosyltransferase-I (M340H-B4Gal-T1) in Complex with Chitotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.224 (Depositor) 
  • R-Value Work: 
    0.202 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Oligosaccharide Preferences of beta1,4-Galactosyltransferase-I: Crystal Structures of Met340His Mutant of Human beta1,4-Galactosyltransferase-I with a Pentasaccharide and Trisaccharides of the N-Glycan Moiety

Ramasamy, V.Ramakrishnan, B.Boeggeman, E.Ratner, D.M.Seeberger, P.H.Qasba, P.K.

(2005) J Mol Biology 353: 53-67

  • DOI: https://doi.org/10.1016/j.jmb.2005.07.050
  • Primary Citation Related Structures: 
    2AE7, 2AEC, 2AES, 2AGD, 2AH9

  • PubMed Abstract: 

    beta-1,4-Galactosyltransferase-I (beta4Gal-T1) transfers galactose from UDP-galactose to N-acetylglucosamine (GlcNAc) residues of the branched N-linked oligosaccharide chains of glycoproteins. In an N-linked biantennary oligosaccharide chain, one antenna is attached to the 3-hydroxyl-(1,3-arm), and the other to the 6-hydroxyl-(1,6-arm) group of mannose, which is beta-1,4-linked to an N-linked chitobiose, attached to the aspargine residue of a protein. For a better understanding of the branch specificity of beta4Gal-T1 towards the GlcNAc residues of N-glycans, we have carried out kinetic and crystallographic studies with the wild-type human beta4Gal-T1 (h-beta4Gal-T1) and the mutant Met340His-beta4Gal-T1 (h-M340H-beta4Gal-T1) in complex with a GlcNAc-containing pentasaccharide and several GlcNAc-containing trisaccharides present in N-glycans. The oligosaccharides used were: pentasaccharide GlcNAcbeta1,2-Manalpha1,6 (GlcNAcbeta1,2-Manalpha1,3)Man; the 1,6-arm trisaccharide, GlcNAcbeta1,2-Manalpha1,6-Manbeta-OR (1,2-1,6-arm); the 1,3-arm trisaccharides, GlcNAcbeta1,2-Manalpha1,3-Manbeta-OR (1,2-1,3-arm) and GlcNAcbeta1,4-Manalpha1,3-Manbeta-OR (1,4-1,3-arm); and the trisaccharide GlcNAcbeta1,4-GlcNAcbeta1,4-GlcNAc (chitotriose). With the wild-type h-beta4Gal-T1, the K(m) of 1,2-1,6-arm is approximately tenfold lower than for 1,2-1,3-arm and 1,4-1,3-arm, and 22-fold lower than for chitotriose. Crystal structures of h-M340H-beta4Gal-T1 in complex with the pentasaccharide and various trisaccharides at 1.9-2.0A resolution showed that beta4Gal-T1 is in a closed conformation with the oligosaccharide bound to the enzyme, and the 1,2-1,6-arm trisaccharide makes the maximum number of interactions with the enzyme, which is in concurrence with the lowest K(m) for the trisaccharide. Present studies suggest that beta4Gal-T1 interacts preferentially with the 1,2-1,6-arm trisaccharide rather than with the 1,2-1,3-arm or 1,4-1,3-arm of a bi- or tri-antennary oligosaccharide chain of N-glycan.


  • Organizational Affiliation
    • Laboratory of Experimental and Computational Biology, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA.

Macromolecule Content 

  • Total Structure Weight: 104.43 kDa 
  • Atom Count: 7,558 
  • Modeled Residue Count: 816 
  • Deposited Residue Count: 861 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-1,4-galactosyltransferase 1
A, B, C
287Homo sapiensMutation(s): 3 
Gene Names: B4GALT1GGTB2
EC: 2.4.1.90 (PDB Primary Data), 2.4.1 (UniProt), 2.4.1.22 (UniProt), 2.4.1.275 (UniProt), 2.4.1.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15291 (Homo sapiens)
Explore P15291 
Go to UniProtKB:  P15291
PHAROS:  P15291
GTEx:  ENSG00000086062 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15291
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F
3N/A
Glycosylation Resources
GlyTouCan: G47362BJ
GlyCosmos: G47362BJ
GlyGen: G47362BJ

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDH

Query on UDH



Download:Ideal Coordinates CCD File
CA [auth C],
G [auth A],
P [auth B]
6-AMINOHEXYL-URIDINE-C1,5'-DIPHOSPHATE
C15 H27 N3 O12 P2
MLWJBKPFDKRHBM-FMKGYKFTSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
LA [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
FA [auth C]
GA [auth C]
HA [auth C]
AA [auth B],
BA [auth B],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
EA [auth C]
I [auth A]
J [auth A]
R [auth B]
S [auth B]
EA [auth C],
I [auth A],
J [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DIO

Query on DIO



Download:Ideal Coordinates CCD File
KA [auth C],
O [auth A]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
DA [auth C],
H [auth A],
Q [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.202 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.501α = 90
b = 195.362β = 90
c = 144.023γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-06
    Changes: Structure summary