DB code: T00415

RLCP classification 3.903.70210.640 : Transfer
CATH domain -.-.-.- :
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A Catalytic domain
3.10.180.20 : 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
E.C. 2.4.1.101
CSA 1foa
M-CSA 1foa
MACiE

CATH domain Related DB codes (homologues)
3.90.550.10 : Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A S00709 S00465 S00466 D00417 D00859 D00860

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq CAZy Pfam
P27115 Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
EC 2.4.1.101
N-glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I
GNT-I
GlcNAc-T I
NP_001076214.1 (Protein)
NM_001082745.1 (DNA/RNA sequence)
GT13 (Glycosyltransferase Family 13)
PF03071 (GNT-I)
[Graphical View]

KEGG enzyme name
Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
N-Acetylglucosaminyltransferase I
N-Glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I
Uridine diphosphoacetylglucosamine-alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase
UDP-N-acetylglucosaminyl:alpha-1,3-D-mannoside-beta-1,2-N-acetylglucosaminyltransferase I
UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I
Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase
GnTI

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P27115 MGAT1_RABIT UDP-N-acetyl-D-glucosamine + 3-(alpha-D-mannosyl)-beta-D-mannosyl-R = UDP + 3-(2-(N-acetyl-beta-D-glucosaminyl)-alpha-D-mannosyl)-beta-D-mannosyl-R. Golgi apparatus membrane, Single-pass type II membrane protein.

KEGG Pathways
Map code Pathways E.C.
MAP01030 Glycan structures - biosynthesis 1
MAP00510 N-Glycan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00034 C00043 C04614 C00015 C04880
E.C.
Compound Manganese UDP-N-acetyl-D-glucosamine 3-(alpha-D-mannosyl)-beta-D-mannosyl-R UDP 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R
Type heavy metal amide group,carbohydrate,nucleotide polysaccharide amide group,nucleotide amide group,polysaccharide
ChEBI 18291
35154
16264
17659
PubChem 23930
445675
6031
1fo8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fo9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1foaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Bound:UD1 Unbound Unbound Unbound
2am3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Analogue:UPG Analogue:GOL_450 Unbound Unbound
2am4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Analogue:U2F Unbound Unbound Unbound
2am5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MN Unbound Unbound Bound:UDP Unbound
2apcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:UDM Analogue:GOL_450 Unbound Unbound
1fo8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1fo9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
1foaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2am3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2am4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2am5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound
2apcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1], [3], [6], [7], [8]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1fo8A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
1fo9A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
1foaA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
2am3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
2am4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
2am5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
2apcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 291 ASP 213(Manganese binding)
1fo8A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1fo9A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1foaA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2am3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2am4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2am5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2apcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.1, p.6383-6385
[3]
Fig.4, p.5272-5273
[6]
Fig.5, p.16924-16937
[7]
p.74-76
[8]
Fig.4, p.527-530

References
[1]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
Medline ID
PubMed ID 10350455
Journal Biochemistry
Year 1999
Volume 38
Pages 6380-5
Authors Charnock SJ, Davies GJ
Title Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.
Related PDB 1qg8 2qg8 3qg8
Related UniProtKB P39621
[2]
Resource
Comments
Medline ID
PubMed ID 10508766
Journal Curr Opin Struct Biol
Year 1999
Volume 9
Pages 563-71
Authors Breton C, Imberty A
Title Structure/function studies of glycosyltransferases.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 11032794
Journal EMBO J
Year 2000
Volume 19
Pages 5269-80
Authors Unligil UM, Zhou S, Yuwaraj S, Sarkar M, Schachter H, Rini JM
Title X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
Related PDB 1fo8 1fo9 1foa
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 12691742
Journal J Mol Biol
Year 2003
Volume 328
Pages 307-17
Authors Coutinho PM, Deleury E, Davies GJ, Henrissat B
Title An evolving hierarchical family classification for glycosyltransferases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 15653326
Journal Trends Biochem Sci
Year 2005
Volume 30
Pages 53-62
Authors Qasba PK, Ramakrishnan B, Boeggeman E
Title Substrate-induced conformational changes in glycosyltransferases.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 17177443
Journal J Am Chem Soc
Year 2006
Volume 128
Pages 16921-7
Authors Kozmon S, Tvaroska I
Title Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 16769084
Journal J Mol Biol
Year 2006
Volume 360
Pages 67-79
Authors Gordon RD, Sivarajah P, Satkunarajah M, Ma D, Tarling CA, Vizitiu D, Withers SG, Rini JM
Title X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.
Related PDB 2am3 2am4 2am5 2apc
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 18518825
Journal Annu Rev Biochem
Year 2008
Volume 77
Pages 521-55
Authors Lairson LL, Henrissat B, Davies GJ, Withers SG
Title Glycosyltransferases: structures, functions, and mechanisms.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to glycosyltransferase family-13 (GT13 family), with a GT-A fold and an inverting mechanism (see [8]).
The structure of the N-terminal domain, which contains the N-terminal cytoplasmic region and a membrane-bound region, has not been determined yet.
According to the literature [3], [7] and [8], this enzyme catalyzes the following reaction:
(0) Manganese ion, bound to Asp213, stabilizes the negative charge on the leaving phosphate groups.
(1) Asp291 acts as a general base to deprotonate O2 atom of the acceptor, mannosyl group, to activate it.
(2) The activated O2 atom of the mannosyl group makes a nucleophilic attack on the C1 atom of N-acetyl-glucosamine of UDP-N-acetyl-D-glucosamine, leading to the transition state, where a positive charge is developed on the C1 atom and negative charges on the O2 atom and the leaving phosphate oxygen.
(3) The bond between the C1 atom and the leaving phosphate group is cleaved while the bond between the O2 atom and the C1 atom is formed. (SN2-like reaction)

Created Updated
2010-01-29 2011-10-04