3CQL - JenaLib

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Title :   CRYSTAL STRUCTURE OF GH FAMILY 19 CHITINASE FROM CARICA PAPAYA

Authors :   J. Huet, P. Rucktoa, B. Clantin, M. Azarkan, Y. Looze, V. Villeret, R. Wi

Date :   03 Apr 08 (Deposition) - 05 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Glycosyl Hydrolase, Chitinase, N-Acetyl-D-Glucosamine, Carbohydrate Metabolism, Chitin Degradation, Chitin-Binding, Glycosidase, Hydrolase, Polysaccharide Degradation, Vacuole (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Huet, P. Rucktooa, B. Clantin, M. Azarkan, Y. Looze, V. Villeret, R. Wintjens
X-Ray Structure Of Papaya Chitinase Reveals The Substrate Binding Mode Of Glycosyl Hydrolase Family 19 Chitinases.
Biochemistry V. 47 8283 2008
PubMed-ID: 18636748 | Reference-DOI: 10.1021/BI800655U
(for further references see the PDB file header)

Molecule 1 - ENDOCHITINASE
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Organism Common	:	MAMON
	Organism Scientific	:	CARICA PAPAYA
	Organism Taxid	:	3649
	Other Details	:	LATEX

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	2	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	-1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
4	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:66 , GLU A:67 , PHE A:86 , LYS A:88 , GLU A:89 , ARG A:90 , GLN A:118 , GLU A:203 , GLN A:211 , ARG A:215 , HOH A:285 , HOH A:300 , HOH A:361	BINDING SITE FOR RESIDUE NDG A 244
02	AC2	SOFTWARE	ILE A:117 , LEU A:119 , SER A:120 , TRP A:121 , TYR A:123 , ASN A:124 , PHE A:157 , LYS A:165 , ILE A:198 , HOH A:270 , HOH A:282 , HOH A:287 , HOH A:319 , HOH A:398 , HOH A:451	BINDING SITE FOR RESIDUE NAG A 245
03	AC3	SOFTWARE	GLY A:217 , ARG A:220 , ARG A:221 , HOH A:313 , HOH A:456 , HOH A:457 , HOH A:458 , HOH A:461	BINDING SITE FOR RESIDUE NDG A 246
04	AC4	SOFTWARE	TRP A:72 , SER A:74 , HIS B:66 , GLU B:67 , PHE B:86 , LYS B:88 , GLU B:89 , ARG B:90 , GLN B:118 , GLU B:203 , GLN B:211 , ARG B:215 , HOH B:279 , HOH B:372	BINDING SITE FOR RESIDUE NAG B 244
05	AC5	SOFTWARE	ILE B:117 , LEU B:119 , SER B:120 , TRP B:121 , TYR B:123 , ASN B:124 , PHE B:157 , LYS B:165 , ILE B:198 , ASN B:199 , HOH B:259 , HOH B:288 , HOH B:292 , HOH B:348 , HOH B:362 , HOH B:431	BINDING SITE FOR RESIDUE NAG B 245
06	AC6	SOFTWARE	GLY B:217 , ARG B:220 , ARG B:221 , GLY B:224 , HOH B:275 , HOH B:415 , HOH B:436 , HOH B:437	BINDING SITE FOR RESIDUE NAG B 246
07	AC7	SOFTWARE	GLN A:13 , ARG A:221 , HOH A:459	BINDING SITE FOR RESIDUE SO4 A 247
08	AC8	SOFTWARE	GLN B:13 , LYS B:16 , ARG B:221 , HOH B:283	BINDING SITE FOR RESIDUE SO4 B 247
09	AC9	SOFTWARE	LYS B:16 , HIS B:17 , ASN B:20 , HOH B:439	BINDING SITE FOR RESIDUE SO4 B 248
10	BC1	SOFTWARE	ARG B:8 , ASP B:12 , ARG B:18 , THR B:30 , TYR B:31 , HOH B:438	BINDING SITE FOR RESIDUE SO4 B 249
11	BC2	SOFTWARE	ARG A:8 , ARG A:18 , ASN A:19 , TYR A:29 , THR A:30 , TYR A:31 , ASP A:32	BINDING SITE FOR RESIDUE GOL A 248

Asymmetric Unit

No.	Residues
1	A:23	-	A:85
2	A:97	-	A:105
3	A:204	-	A:236
4	B:23	-	B:85
5	B:97	-	B:105
6	B:204	-	B:236

Asymmetric Unit

No.	Residues
1	Ala A:163	-	Pro A:164
2	Ala B:163	-	Pro B:164

(no "SAP(SNP)/Variant" information available for 3CQL)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_19_1	PS00773	Chitinases family 19 signature 1.	CHIT_CARPA	23-45	2	A:23-45 B:23-45
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHIT_CARPA	149-159	2	A:150-159 B:150-159

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_19_1	PS00773	Chitinases family 19 signature 1.	CHIT_CARPA	23-45	1	A:23-45 -
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHIT_CARPA	149-159	1	A:150-159 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_19_1	PS00773	Chitinases family 19 signature 1.	CHIT_CARPA	23-45	1	- B:23-45
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHIT_CARPA	149-159	1	- B:150-159

(no "Exon" information available for 3CQL)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:243
 aligned with CHIT_CARPA | P85084 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           CHIT_CARPA     1 GIEKIISRSMFDQMLKHRNNPACPAKGFYTYDAFLAAAKSFPSFGTTGSTDVRKRELAAFLGQTSHETTGGWPSAPDGPYAWGYCFLKERNPSSNYCAPSPRYPCAPGKSYYGRGPLQLSWNYNYGPCGEALRVNLLGNPDLVATDRVLSFKTALWFWMTPQAPKPSCHDVLTGRWQPSAADTAAGRLPGYGVLTNLLNGGLECGKGPNPQVADRLGFFRRYCGLLGVGTGNNLDCYNQRPFG 243
               SCOP domains d3cqla_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------3cqlA02 A:88-145 Endochitinase, domain 2                  -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cql A   1 GIEKIISRSMFDQMLKHRNNPACPAKGFYTYDAFIAAAKSFPSFGTTGSTDVRKREIAAFLGQTSHETTGGWPSAPDGPYAWGYCFLKERNPSSNYCAPSPRYPCAPGKSYYGRGPIQLSWNYNYGPCGEALRVNLLGNPDLVATDRVISFKTALWFWMTPQAPKPSCHDVITGRWQPSAADTAAGRLPGYGVITNIINGGLECGKGPNPQVADRIGFFRRYCGILGVGTGNNLDCYNQRPFG 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with CHIT_CARPA | P85084 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           CHIT_CARPA     1 GIEKIISRSMFDQMLKHRNNPACPAKGFYTYDAFLAAAKSFPSFGTTGSTDVRKRELAAFLGQTSHETTGGWPSAPDGPYAWGYCFLKERNPSSNYCAPSPRYPCAPGKSYYGRGPLQLSWNYNYGPCGEALRVNLLGNPDLVATDRVLSFKTALWFWMTPQAPKPSCHDVLTGRWQPSAADTAAGRLPGYGVLTNLLNGGLECGKGPNPQVADRLGFFRRYCGLLGVGTGNNLDCYNQRPFG 243
               SCOP domains d3cqlb_ B: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains ---------------------------------------------------------------------------------------3cqlB02 B:88-145 Endochitinase, domain 2                  -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.hhhhhhhhh..............hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cql B   1 GIEKIISRSMFDQMLKHRNNPACPAKGFYTYDAFIAAAKSFPSFGTTGSTDVRKREIAAFLGQTSHETTGGWPSAPDGPYAWGYCFLKERNPSSNYCAPSPRYPCAPGKSYYGRGPIQLSWNYNYGPCGEALRVNLLGNPDLVATDRVISFKTALWFWMTPQAPKPSCHDVITGRWQPSAADTAAGRLPGYGVITNIINGGLECGKGPNPQVADRIGFFRRYCGILGVGTGNNLDCYNQRPFG 243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: Family 19 glycosidase (12)

Protein domain: automated matches (9)

Papaya (Carica papaya) [TaxId: 3649] (1)

1a	d3cqla_	A:
1b	d3cqlb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Endochitinase; domain 2 (16)

Homologous Superfamily: Endochitinase, domain 2 (16)

Mamon (Carica papaya) (1)

1a	3cqlA02	A:88-145
1b	3cqlB02	B:88-145

(no "Pfam Domain" information available for 3CQL)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHIT_CARPA | P85084)

molecular function
	GO:0008061	chitin binding	Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	GO:0004568	chitinase activity	Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0006032	chitin catabolic process	The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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