EzCatDB: T00063
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DB codeT00063
RLCP classification1.32.5000.73 : Hydrolysis
CATH domainDomain 12.60.40.10 : Immunoglobulin-like
Domain 23.20.20.80 : TIM BarrelCatalytic domain
Domain 33.10.50.10 : Chitinase A; domain 3
E.C.3.2.1.14
CSA1ctn

CATH domainRelated DB codes (homologues)
2.60.40.10 : Immunoglobulin-likeM00131,T00257,T00005,M00113,M00127,M00132,M00323,M00325,M00327,M00329,M00330,M00331,M00332,T00307,D00166,D00500,M00112,M00193,T00065,T00067,T00245
3.10.50.10 : Chitinase A; domain 3M00134
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

P07254
Protein nameChitinase Achitinase
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
SynonymsEC 3.2.1.14
PfamPF08329 (ChitinaseA_N)
PF00704 (Glyco_hydro_18)
[Graphical view]
CAZyGH18 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00530Aminosugars metabolism

UniProtKB:Accession NumberP07254
Entry nameCHIA_SERMA
ActivityRandom hydrolysis of N-acetyl-beta-D- glucosaminide (1->4)-beta-linkages in chitin and chitodextrins.
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00461C00851C00001C03518C00140C00461
CompoundChitinChitodextrinH2ON-Acetyl-D-glucosaminideN-Acetyl-D-glucosamineChitin
Typeamide group,polysaccharideamide group,polysaccharideH2Oamide group,carbohydrateamide group,carbohydrateamide group,polysaccharide
ChEBI

15377

506227


PubChem

962
22247451

439174


               
1ctnA01UnboundUnbound UnboundUnboundUnboundUnbound
1edqA01UnboundUnbound UnboundUnboundUnboundUnbound
1ehnA01UnboundUnbound UnboundUnboundUnboundUnbound
1eibA01UnboundUnbound UnboundUnboundUnboundUnbound
1ffrA01UnboundUnbound UnboundUnboundUnboundUnbound
1k9tA01UnboundUnbound UnboundUnboundUnboundUnbound
1nh6A01UnboundUnbound UnboundUnboundUnboundUnbound
1ctnA02UnboundUnbound UnboundUnboundUnboundUnbound
1edqA02UnboundUnbound UnboundUnboundUnboundUnbound
1ehnA02Bound:NAG-NAG-NAG-NAG-NAG-NAG-NAG-NAGUnbound UnboundUnboundUnboundUnbound
1eibA02Bound:NAG-NAG-NAG-NAG-NAG-NAG-NAG-NAGUnbound UnboundUnboundUnboundUnbound
1ffrA02UnboundUnbound UnboundUnboundUnboundTransition-state-bound:NAG-NAG-NAG-NAG-NAG(chain B),NAG-NAG(chain C)
1k9tA02Bound:NAG-NAG-NAG-NAGUnbound UnboundUnboundUnboundUnbound
1nh6A02Bound:NAG-NAG-NAG-NAG-NAG-NAGUnbound UnboundUnboundUnboundUnbound
1ctnA03UnboundUnbound UnboundUnboundUnboundUnbound
1edqA03UnboundUnbound UnboundUnboundUnboundUnbound
1ehnA03UnboundUnbound UnboundUnboundUnboundUnbound
1eibA03UnboundUnbound UnboundUnboundUnboundUnbound
1ffrA03UnboundUnbound UnboundUnboundUnboundUnbound
1k9tA03UnboundUnbound UnboundUnboundUnboundUnbound
1nh6A03UnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [6]
pdbCatalytic residuescomment
          
1ctnA01 
 
1edqA01 
 
1ehnA01 
 
1eibA01 
 
1ffrA01 
 
1k9tA01 
 
1nh6A01 
 
1ctnA02ASP 313;GLU 315;TYR 390;ASP 391
 
1edqA02ASP 313;GLU 315;TYR 390;ASP 391
 
1ehnA02ASP 313;       ;TYR 390;ASP 391
mutant E315Q
1eibA02       ;GLU 315;TYR 390;ASP 391
mutant D313A
1ffrA02ASP 313;GLU 315;       ;ASP 391
mutant Y390F
1k9tA02ASP 313;GLU 315;TYR 390;       
mutant D391A
1nh6A02ASP 313;       ;TYR 390;ASP 391
mutant E315L
1ctnA03 
 
1edqA03 
 
1ehnA03 
 
1eibA03 
 
1ffrA03 
 
1k9tA03 
 
1nh6A03 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.202-203
[6]Scheme 1, p.11341-113432
[8]p.403

references
[1]
CommentsREVISIONS, AND X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID95219379
PubMed ID7704527
JournalStructure
Year1994
Volume2
Pages1169-80
AuthorsPerrakis A, Tews I, Dauter Z, Oppenheim AB, Chet I, Wilson KS, Vorgias CE
TitleCrystal structure of a bacterial chitinase at 2.3 A resolution.
Related PDB1ctn
Related UniProtKBP07254
[2]
PubMed ID8831791
JournalJ Mol Biol
Year1996
Volume262
Pages243-57
AuthorsTerwisscha van Scheltinga AC, Hennig M, Dijkstra BW
TitleThe 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.
[3]
PubMed ID9377712
JournalFold Des
Year1997
Volume2
Pages291-4
AuthorsPerrakis A, Ouzounis C, Wilson KS
TitleEvolution of immunoglobulin-like modules in chitinases: their structural flexibility and functional implications.
[4]
PubMed ID10794597
JournalIUBMB Life
Year1999
Volume48
Pages199-204
AuthorsLin FP, Chen HC, Lin CS
TitleSite-directed mutagenesis of Asp313, Glu315, and Asp391 residues in chitinase of Aeromonas caviae.
[5]
PubMed ID10823940
JournalProc Natl Acad Sci U S A
Year2000
Volume97
Pages5842-7
Authorsvan Aalten DM, Synstad B, Brurberg MB, Hough E, Riise BW, Eijsink VG, Wierenga RK
TitleStructure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution.
[6]
CommentsX-ray crystallography
PubMed ID11560481
JournalBiochemistry
Year2001
Volume40
Pages11338-43
AuthorsPapanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, Petratos K
TitleHigh resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
Related PDB1ehn,1eib,1ffr
[7]
PubMed ID11342059
JournalBiochim Biophys Acta
Year2001
Volume1545
Pages349-56
AuthorsLonhienne T, Baise E, Feller G, Bouriotis V, Gerday C
TitleEnzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.
[8]
CommentsX-ray crystallography
PubMed ID12554965
JournalActa Crystallogr D Biol Crystallogr
Year2003
Volume59
Pages400-3
AuthorsPapanikolau Y, Tavlas G, Vorgias CE, Petratos K
TitleDe novo purification scheme and crystallization conditions yield high-resolution structures of chitinase A and its complex with the inhibitor allosamidin.
Related PDB1edq
[9]
PubMed ID12932195
JournalBiochem J
Year2003
Volume376
Pages87-95
AuthorsAronson NN Jr, Halloran BA, Alexyev MF, Amable L, Madura JD, Pasupulati L, Worth C, Van Roey P
TitleFamily 18 chitinase-oligosaccharide substrate interaction: subsite preference and anomer selectivity of Serratia marcescens chitinase A.
Related PDB1nh6

comments
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.
(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.
However, the mutation of Asp391 inactivates this enzyme, suggesting that the residue must be involved in catalysis (see Table 1 of [6]).

createdupdated
2004-04-302009-02-26


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Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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