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

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.
MAP00510	N-Glycan biosynthesis
MAP01030	Glycan structures - biosynthesis 1

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 18291 35154	16264 16264		17659 17659
PubChem	23930 23930	445675 445675		6031 6031

1fo8A01	Unbound	Unbound	Unbound	Unbound	Unbound
1fo9A01	Unbound	Unbound	Unbound	Unbound	Unbound
1foaA01	Bound:_MN	Bound:UD1	Unbound	Unbound	Unbound
2am3A01	Bound:_MN	Analogue:UPG	Analogue:GOL_450	Unbound	Unbound
2am4A01	Bound:_MN	Analogue:U2F	Unbound	Unbound	Unbound
2am5A01	Bound:_MN	Unbound	Unbound	Bound:UDP	Unbound
2apcA01	Unbound	Analogue:UDM	Analogue:GOL_450	Unbound	Unbound
1fo8A02	Unbound	Unbound	Unbound	Unbound	Unbound
1fo9A02	Unbound	Unbound	Unbound	Unbound	Unbound
1foaA02	Unbound	Unbound	Unbound	Unbound	Unbound
2am3A02	Unbound	Unbound	Unbound	Unbound	Unbound
2am4A02	Unbound	Unbound	Unbound	Unbound	Unbound
2am5A02	Unbound	Unbound	Unbound	Unbound	Unbound
2apcA02	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	ASP 291	ASP 213(Manganese binding)
1fo9A01	ASP 291	ASP 213(Manganese binding)
1foaA01	ASP 291	ASP 213(Manganese binding)
2am3A01	ASP 291	ASP 213(Manganese binding)
2am4A01	ASP 291	ASP 213(Manganese binding)
2am5A01	ASP 291	ASP 213(Manganese binding)
2apcA01	ASP 291	ASP 213(Manganese binding)
1fo8A02
1fo9A02
1foaA02
2am3A02
2am4A02
2am5A02
2apcA02

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)

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