T00063
type: Enzyme
rlcp: p73
cath: Immunoglobulin-like
cath: TIM Barrel
cath: Chitinase A; domain 3
ec: https://purl.uniprot.org/enzyme/3.2.1.14
csa: 1ctn
uniprot: P07254
kegg enzyme: chitinase
kegg enzyme: chitodextrinase
kegg enzyme: 1,4-beta-poly-N-acetylglucosaminidase
kegg enzyme: poly-beta-glucosaminidase
kegg enzyme: beta-1,4-poly-N-acetyl glucosamidinase
kegg enzyme: poly[1,4-(N-acetyl-beta-D-glucosaminide)] glycanohydrolase
kegg pathway: Aminosugars metabolism
kegg substrate: Chitin
kegg substrate: Chitodextrin
kegg substrate: H2O
kegg product: N-Acetyl-D-glucosaminide
kegg product: N-Acetyl-D-glucosamine
kegg product: Chitin
pdb: 1ctnA01
pdb: 1edqA01
pdb: 1ehnA01
pdb: 1eibA01
pdb: 1ffrA01
pdb: 1k9tA01
pdb: 1nh6A01
pdb: 1ctnA02
pdb: 1edqA02
pdb: 1ehnA02
pdb: 1eibA02
pdb: 1ffrA02
pdb: 1k9tA02
pdb: 1nh6A02
pdb: 1ctnA03
pdb: 1edqA03
pdb: 1ehnA03
pdb: 1eibA03
pdb: 1ffrA03
pdb: 1k9tA03
pdb: 1nh6A03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ctnA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1edqA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ehnA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1eibA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ffrA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1k9tA01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1nh6A01
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ctnA02
pdb bound state: Unbound
  compound: Chitin
  pdb: 1edqA02
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ffrA02
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ctnA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1edqA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ehnA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1eibA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1ffrA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1k9tA03
pdb bound state: Unbound
  compound: Chitin
  pdb: 1nh6A03
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1ctnA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1edqA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1ehnA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1eibA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1ffrA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1k9tA01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1nh6A01
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1ctnA02
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1edqA02
pdb bound state: Unbound
  compound: Chitodextrin
  pdb: 1ehnA02
active site residues resources: Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.
references: Crystal structure of a bacterial chitinase at 2.3 A resolution.
references: The 1.8 A resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18.
references: Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications.
references: Site-directed mutagenesis of Asp313, Glu315, and Asp391 residues in chitinase of Aeromonas caviae.
references: Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
references: High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
references: Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.
references: De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin.
references: Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A.
comment: (5) The deprotonated sidechain of Glu315 acts as a general base, abstracting the water molecule, which can act on the C1 carbon at subsite (-1). Taken together, Glu315 acts as an acid-base, whilst Asp313 modulates the role of Glu315. Moreover, Tyr390 stabilizes the transition-state through the water. The stabilization might be assisted by N-acetyl group of the substrate. This enzyme is composed of the N-terminal immunoglobulin-like region and the C-terminal catalytic region, which has also two distinct domains. According to the literature [3], the N-terminal immunoglobulin-like domain might interact with the chitin substrate during catalysis. In the early study [4], Asp313, Glu315 and Asp391 have been thought to be involved in catalysis. The paper [4] suggested that Asp313 and Glu315 might act as a stabilizer and a general acid, respectively. According to the more recent work ([6] & [8]), however, Tyr390 was reported to be involved in the catalytic reaction, instead of Asp391. The paper [6] proposed the following mechanism: (1) The sugar unit at the subsite (-1) adopts a boat conformation, which has higher free energy by 8kcal/mol, and its N-acetyl group points toward Asp313 and Glu315. The side chain of Asp313 points toward Asp311, away from Glu315. A water molecule is hydrogen-bonded to the phenol hydroxyl group of Tyr390 and the amine group of the acetamido group of the sugar unit at the subsite (-1). The sidechain carboxylate of Glu315 is protonated. (2) Glu315 functions as a general acid, and protonates the O4 oxygen of the sugar unit at the subsite (+1), thus cleaving the glycosidic linkage, O4(+1)-C1(-1). (This suggests SN1-like cleavage.) (3) The positive charge is developed on C1 and O5 atoms at the subsite (-1), which can be stabilized by the water molecule hydrogen-bonded to Tyr390 and the acetamido group at (-1), the O7 atom of the acetamido group at (-1), and the deprotonated sidechain of Glu315. (4) This cleavage induces the rotation of Asp313 toward G…

Immunoglobulin-like
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/2.60.40.10

TIM Barrel
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.20.20.80
catalytic domain: index.html

Chitinase A; domain 3
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.10.50.10

Aminosugars metabolism
type: KeggPathway
references: KEGG:MAP00530

Chitin
type: KeggSubstrate
references: KEGG:C00461
compound type: amide group
compound type: polysaccharide
type: KeggProduct

Chitodextrin
type: KeggSubstrate
references: KEGG:C00851
compound type: amide group
compound type: polysaccharide

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

N-Acetyl-D-glucosaminide
type: KeggProduct
references: KEGG:C03518
compound type: amide group
compound type: carbohydrate

N-Acetyl-D-glucosamine
type: KeggProduct
references: KEGG:C00140
compound type: amide group
compound type: carbohydrate
references: CHEBI:506227
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1ctnA02
type: Pdb
references: 1ctn
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ctn
catalytic residue: ASP 313;GLU 315;TYR 390;ASP 391

1edqA02
type: Pdb
references: 1edq
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1edq
catalytic residue: ASP 313;GLU 315;TYR 390;ASP 391

1ehnA02
type: Pdb
references: 1ehn
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ehn
catalytic residue: ASP 313; ;TYR 390;ASP 391
comment: mutant E315Q

1eibA02
type: Pdb
references: 1eib
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1eib
catalytic residue: ;GLU 315;TYR 390;ASP 391
comment: mutant D313A

1ffrA02
type: Pdb
references: 1ffr
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1ffr
catalytic residue: ASP 313;GLU 315; ;ASP 391
comment: mutant Y390F

1k9tA02
type: Pdb
references: 1k9t
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1k9t
catalytic residue: ASP 313;GLU 315;TYR 390;
comment: mutant D391A

1nh6A02
type: Pdb
references: 1nh6
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nh6
catalytic residue: ASP 313; ;TYR 390;ASP 391
comment: mutant E315L

Crystal structure of a bacterial chitinase at 2.3 A resolution.
type: BibliographicResource
comment: REVISIONS, AND X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
medline id: 95219379
references: http://www.ncbi.nlm.nih.gov/pubmed/7704527
journal: Structure
volume: 2
pages: 1169-80
published year: 1994
authors:
  item: Perrakis A
  item: Tews I
  item: Dauter Z
  item: Oppenheim AB
  item: Chet I
  item: Wilson KS
  item: Vorgias CE
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P07254

The 1.8 A resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8831791
journal: J Mol Biol
volume: 262
pages: 243-57
published year: 1996
authors:
  item: Terwisscha van Scheltinga AC
  item: Hennig M
  item: Dijkstra BW

Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9377712
journal: Fold Des
volume: 2
pages: 291-4
published year: 1997
authors:
  item: Perrakis A
  item: Ouzounis C
  item: Wilson KS

Site-directed mutagenesis of Asp313, Glu315, and Asp391 residues in chitinase of Aeromonas caviae.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10794597
journal: IUBMB Life
volume: 48
pages: 199-204
published year: 1999
authors:
  item: Lin FP
  item: Chen HC
  item: Lin CS

Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10823940
journal: Proc Natl Acad Sci U S A
volume: 97
pages: 5842-7
published year: 2000
authors:
  item: van Aalten DM
  item: Synstad B
  item: Brurberg MB
  item: Hough E
  item: Riise BW
  item: Eijsink VG
  item: Wierenga RK

High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/11560481
journal: Biochemistry
volume: 40
pages: 11338-43
published year: 2001
authors:
  item: Papanikolau Y
  item: Prag G
  item: Tavlas G
  item: Vorgias CE
  item: Oppenheim AB
  item: Petratos K
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11342059
journal: Biochim Biophys Acta
volume: 1545
pages: 349-56
published year: 2001
authors:
  item: Lonhienne T
  item: Baise E
  item: Feller G
  item: Bouriotis V
  item: Gerday C

De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin.
type: BibliographicResource
comment: X-ray crystallography
references: http://www.ncbi.nlm.nih.gov/pubmed/12554965
journal: Acta Crystallogr D Biol Crystallogr
volume: 59
pages: 400-3
published year: 2003
authors:
  item: Papanikolau Y
  item: Tavlas G
  item: Vorgias CE
  item: Petratos K
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12932195
journal: Biochem J
volume: 376
pages: 87-95
published year: 2003
authors:
  item: Aronson NN Jr
  item: Halloran BA
  item: Alexyev MF
  item: Amable L
  item: Madura JD
  item: Pasupulati L
  item: Worth C
  item: Van Roey P
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl

TransitionStateBound
pdb: 1ffrA02
ligand het code: NAG-NAG-NAG-NAG-NAG (chain B), NAG-NAG (chain C)

ReferenceForCatalyticMechanism
reference index: 4
reference section: p.202-203

ReferenceForCatalyticMechanism
reference index: 6
reference section: Scheme 1, p.11341-11343
reference step: 2

ReferenceForCatalyticMechanism
reference index: 8
reference section: p.403