T00415
type: Enzyme
rlcp: p640
cath: http://ezcatdb.cbrc.jp/EzCatDB/cath/-.-.-.-
cath: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
cath: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
ec: https://purl.uniprot.org/enzyme/2.4.1.101
csa: 1foa
uniprot: P27115
kegg enzyme: Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
kegg enzyme: N-Acetylglucosaminyltransferase I
kegg enzyme: N-Glycosyl-oligosaccharide-glycoprotein N-acetylglucosaminyltransferase I
kegg enzyme: Uridine diphosphoacetylglucosamine-alpha-1,3-mannosylglycoprotein beta-1,2-N-acetylglucosaminyltransferase
kegg enzyme: UDP-N-acetylglucosaminyl:alpha-1,3-D-mannoside-beta-1,2-N-acetylglucosaminyltransferase I
kegg enzyme: UDP-N-acetylglucosaminyl:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I
kegg enzyme: Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase
kegg enzyme: GnTI
kegg pathway: N-Glycan biosynthesis
kegg pathway: Glycan structures - biosynthesis 1
kegg cofactor: Manganese
kegg substrate: UDP-N-acetyl-D-glucosamine
kegg substrate: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
kegg product: UDP
kegg product: 3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R
pdb: 1fo8A01
pdb: 1fo9A01
pdb: 1foaA01
pdb: 2am3A01
pdb: 2am4A01
pdb: 2am5A01
pdb: 2apcA01
pdb: 1fo8A02
pdb: 1fo9A02
pdb: 1foaA02
pdb: 2am3A02
pdb: 2am4A02
pdb: 2am5A02
pdb: 2apcA02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 1fo8A01
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 1fo9A01
pdb bound state: Analogue
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am3A01
  ligand het code: UPG
pdb bound state: Analogue
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am4A01
  ligand het code: U2F
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am5A01
pdb bound state: Analogue
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2apcA01
  ligand het code: UDM
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 1fo8A02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 1fo9A02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 1foaA02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am3A02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am4A02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2am5A02
pdb bound state: Unbound
  compound: UDP-N-acetyl-D-glucosamine
  pdb: 2apcA02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1fo8A01
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1fo9A01
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1foaA01
pdb bound state: Analogue
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am3A01
  ligand het code: GOL_450
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am4A01
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am5A01
pdb bound state: Analogue
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2apcA01
  ligand het code: GOL_450
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1fo8A02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1fo9A02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 1foaA02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am3A02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am4A02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2am5A02
pdb bound state: Unbound
  compound: 3-(alpha-D-mannosyl)-beta-D-mannosyl-R
  pdb: 2apcA02
pdb bound state: Unbound
  compound: Manganese
  pdb: 1fo8A01
pdb bound state: Unbound
  compound: Manganese
  pdb: 1fo9A01
active site residues resources: Structure/function studies of glycosyltransferases.
active site residues resources: An evolving hierarchical family classification for glycosyltransferases.
active site residues resources: X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.
active site residues resources: Glycosyltransferases: structures, functions, and mechanisms.
active site residues resources: http://ezcatdb.cbrc.jp/EzCatDB/reference/T00415#9
references: Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.
references: Structure/function studies of glycosyltransferases.
references: X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
references: An evolving hierarchical family classification for glycosyltransferases.
references: Substrate-induced conformational changes in glycosyltransferases.
references: Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I.
references: X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.
references: Glycosyltransferases: structures, functions, and mechanisms.
comment: 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)

Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.90.550.10
catalytic domain: index.html

2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.10.180.20

N-Glycan biosynthesis
type: KeggPathway
references: KEGG:MAP00510

Glycan structures - biosynthesis 1
type: KeggPathway
references: KEGG:MAP01030

Manganese
type: KeggCofactor
references: KEGG:C00034
compound type: heavy metal
references: CHEBI:18291
references: CHEBI:35154
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

UDP-N-acetyl-D-glucosamine
type: KeggSubstrate
references: KEGG:C00043
compound type: amide group
compound type: carbohydrate
compound type: nucleotide
references: CHEBI:16264
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-(alpha-D-mannosyl)-beta-D-mannosyl-R
type: KeggSubstrate
references: KEGG:C04614
compound type: polysaccharide

UDP
type: KeggProduct
references: KEGG:C00015
compound type: amide group
compound type: nucleotide
references: CHEBI:17659
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

3-(2-[N-acetyl-beta-D-glucosaminyl]-alpha-D-mannosyl)-beta-D-mannosyl-R
type: KeggProduct
references: KEGG:C04880
compound type: amide group
compound type: polysaccharide

1fo8A01
type: Pdb
references: 1fo8
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fo8
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

1fo9A01
type: Pdb
references: 1fo9
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1fo9
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

1foaA01
type: Pdb
references: 1foa
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1foa
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

2am3A01
type: Pdb
references: 2am3
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2am3
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

2am4A01
type: Pdb
references: 2am4
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2am4
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

2am5A01
type: Pdb
references: 2am5
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2am5
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

2apcA01
type: Pdb
references: 2apc
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:2apc
catalytic residue: ASP 291
cofactor binding residue: ASP 213(Manganese binding)

Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS).
references: http://www.ncbi.nlm.nih.gov/pubmed/10350455
journal: Biochemistry
volume: 38
pages: 6380-5
published year: 1999
authors:
  item: Charnock SJ
  item: Davies GJ
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P39621

Structure/function studies of glycosyltransferases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10508766
journal: Curr Opin Struct Biol
volume: 9
pages: 563-71
published year: 1999
authors:
  item: Breton C
  item: Imberty A

X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11032794
journal: EMBO J
volume: 19
pages: 5269-80
published year: 2000
authors:
  item: Unligil UM
  item: Zhou S
  item: Yuwaraj S
  item: Sarkar M
  item: Schachter H
  item: Rini JM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

An evolving hierarchical family classification for glycosyltransferases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12691742
journal: J Mol Biol
volume: 328
pages: 307-17
published year: 2003
authors:
  item: Coutinho PM
  item: Deleury E
  item: Davies GJ
  item: Henrissat B

Substrate-induced conformational changes in glycosyltransferases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15653326
journal: Trends Biochem Sci
volume: 30
pages: 53-62
published year: 2005
authors:
  item: Qasba PK
  item: Ramakrishnan B
  item: Boeggeman E

Catalytic mechanism of glycosyltransferases: hybrid quantum mechanical/molecular mechanical study of the inverting N-acetylglucosaminyltransferase I.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/17177443
journal: J Am Chem Soc
volume: 128
pages: 16921-7
published year: 2006
authors:
  item: Kozmon S
  item: Tvaroska I

X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I (GnT I) in complex with donor substrate analogues.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/16769084
journal: J Mol Biol
volume: 360
pages: 67-79
published year: 2006
authors:
  item: Gordon RD
  item: Sivarajah P
  item: Satkunarajah M
  item: Ma D
  item: Tarling CA
  item: Vizitiu D
  item: Withers SG
  item: Rini JM
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Glycosyltransferases: structures, functions, and mechanisms.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/18518825
journal: Annu Rev Biochem
volume: 77
pages: 521-55
published year: 2008
authors:
  item: Lairson LL
  item: Henrissat B
  item: Davies GJ
  item: Withers SG

ReferenceForCatalyticMechanism
reference index: 1
reference section: Fig.1, p.6383-6385

ReferenceForCatalyticMechanism
reference index: 3
reference section: Fig.4, p.5272-5273

ReferenceForCatalyticMechanism
reference index: 6
reference section: Fig.5, p.16924-16937

ReferenceForCatalyticMechanism
reference index: 7
reference section: p.74-76

ReferenceForCatalyticMechanism
reference index: 8
reference section: Fig.4, p.527-530