DB code: T00063

RLCP classification 1.32.5000.73 : Hydrolysis
CATH domain 2.60.40.10 : Immunoglobulin-like
3.20.20.80 : TIM Barrel Catalytic domain
3.10.50.10 : Chitinase A; domain 3
E.C. 3.2.1.14
CSA 1ctn
M-CSA 1ctn
MACiE

CATH domain Related DB codes (homologues)
3.10.50.10 : Chitinase A; domain 3 M00134
2.60.40.10 : Immunoglobulin-like M00131 T00257 T00005 M00113 M00127 M00132 M00323 M00325 M00327 M00329 M00330 M00331 M00332 T00307 D00166 D00500 M00112 M00193 T00065 T00067 T00245
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 M00160 D00479 S00204 S00205 S00206 S00207 S00203 S00208 S00209 S00211 S00213 S00214 M00113 T00307 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
P07254 Chitinase A
EC 3.2.1.14
GH18 (Glycoside Hydrolase Family 18)
PF08329 (ChitinaseA_N)
PF00704 (Glyco_hydro_18)
[Graphical View]

KEGG enzyme name
chitinase
chitodextrinase
1,4-beta-poly-N-acetylglucosaminidase
poly-beta-glucosaminidase
beta-1,4-poly-N-acetyl glucosamidinase
poly[1,4-(N-acetyl-beta-D-glucosaminide)] glycanohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07254 CHIA_SERMA Random hydrolysis of N-acetyl-beta-D- glucosaminide (1->4)-beta-linkages in chitin and chitodextrins.

KEGG Pathways
Map code Pathways E.C.
MAP00530 Aminosugars metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00461 C00851 C00001 C03518 C00140 C00461
E.C.
Compound Chitin Chitodextrin H2O N-Acetyl-D-glucosaminide N-Acetyl-D-glucosamine Chitin
Type amide group,polysaccharide amide group,polysaccharide H2O amide group,carbohydrate amide group,carbohydrate amide group,polysaccharide
ChEBI 15377
506227
PubChem 962
22247451
439174
1ctnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1edqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ehnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1eibA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ffrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1k9tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1nh6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ctnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1edqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ehnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NAG-NAG-NAG-NAG-NAG-NAG-NAG-NAG Unbound Unbound Unbound Unbound Unbound
1eibA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NAG-NAG-NAG-NAG-NAG-NAG-NAG-NAG Unbound Unbound Unbound Unbound Unbound
1ffrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Transition-state-bound:NAG-NAG-NAG-NAG-NAG (chain B), NAG-NAG (chain C)
1k9tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NAG-NAG-NAG-NAG Unbound Unbound Unbound Unbound Unbound
1nh6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:NAG-NAG-NAG-NAG-NAG-NAG Unbound Unbound Unbound Unbound Unbound
1ctnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1edqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ehnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1eibA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1ffrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1k9tA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
1nh6A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [6]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ctnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1edqA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ehnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eibA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ffrA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1k9tA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nh6A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ctnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;GLU 315;TYR 390;ASP 391
1edqA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;GLU 315;TYR 390;ASP 391
1ehnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;;TYR 390;ASP 391 mutant E315Q
1eibA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;GLU 315;TYR 390;ASP 391 mutant D313A
1ffrA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;GLU 315;;ASP 391 mutant Y390F
1k9tA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;GLU 315;TYR 390; mutant D391A
1nh6A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 313;;TYR 390;ASP 391 mutant E315L
1ctnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1edqA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ehnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1eibA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ffrA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1k9tA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nh6A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.202-203
[6]
Scheme 1, p.11341-11343 2
[8]
p.403

References
[1]
Resource
Comments REVISIONS, AND X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 95219379
PubMed ID 7704527
Journal Structure
Year 1994
Volume 2
Pages 1169-80
Authors Perrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE
Title Crystal structure of a bacterial chitinase at 2.3 A resolution.
Related PDB 1ctn
Related UniProtKB P07254
[2]
Resource
Comments
Medline ID
PubMed ID 8831791
Journal J Mol Biol
Year 1996
Volume 262
Pages 243-57
Authors Terwisscha van Scheltinga AC, Hennig M, Dijkstra BW
Title 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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9377712
Journal Fold Des
Year 1997
Volume 2
Pages 291-4
Authors Perrakis A, Ouzounis C, Wilson KS
Title Evolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 10794597
Journal IUBMB Life
Year 1999
Volume 48
Pages 199-204
Authors Lin FP, Chen HC, Lin CS
Title Site-directed mutagenesis of Asp313, Glu315, and Asp391 residues in chitinase of Aeromonas caviae.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 10823940
Journal Proc Natl Acad Sci U S A
Year 2000
Volume 97
Pages 5842-7
Authors van Aalten DM, Synstad B, Brurberg MB, Hough E, Riise BW, Eijsink VG, Wierenga RK
Title Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11560481
Journal Biochemistry
Year 2001
Volume 40
Pages 11338-43
Authors Papanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, Petratos K
Title High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
Related PDB 1ehn 1eib 1ffr
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 11342059
Journal Biochim Biophys Acta
Year 2001
Volume 1545
Pages 349-56
Authors Lonhienne T, Baise E, Feller G, Bouriotis V, Gerday C
Title Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 12554965
Journal Acta Crystallogr D Biol Crystallogr
Year 2003
Volume 59
Pages 400-3
Authors Papanikolau Y, Tavlas G, Vorgias CE, Petratos K
Title De novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin.
Related PDB 1edq
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12932195
Journal Biochem J
Year 2003
Volume 376
Pages 87-95
Authors Aronson NN Jr, Halloran BA, Alexyev MF, Amable L, Madura JD, Pasupulati L, Worth C, Van Roey P
Title Family 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A.
Related PDB 1nh6
Related UniProtKB

Comments
(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 Glu315, and the rotation of the acetamido group at (-1) toward Tyr390. The rotation of the acetamido group translocates the water molecule bound to Tyr390 closer to Glu315.
However, the mutation of Asp391 inactivates this enzyme, suggesting that the residue must be involved in catalysis (see Table 1 of [6]).

Created Updated
2004-04-30 2009-02-26