3IWR - JenaLib

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Title :   CRYSTAL STRUCTURE OF CLASS I CHITINASE FROM ORYZA SATIVA L. JAPONICA

Authors :   Y. Kezuka, T. Watanabe, T. Nonaka

Date :   03 Sep 09 (Deposition) - 21 Apr 10 (Release) - 30 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.57

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

Keywords :   Class I Chitinase, Oryza Sativa L. Japonica, Chitin-Binding, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kezuka, M. Kojima, R. Mizuno, K. Suzuki, T. Watanabe, T. Nonaka
Structure Of Full-Length Class I Chitinase From Rice Revealed By X-Ray Crystallography And Small-Angle X-Ray Scattering.
Proteins V. 78 2295 2010
PubMed-ID: 20544965 | Reference-DOI: 10.1002/PROT.22742
(for further references see the PDB file header)

Molecule 1 - CHITINASE
	Chains	:	A, B
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B(+)
	Expression System Strain	:	ORIGAMI B(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CHITINASE 2, RESIDUES 33-340
	Gene	:	CHT-2, OSJ_18467
	Organism Common	:	JAPANESE RICE
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Synonym	:	ENDOCHITINASE

		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 (2, 4)

No.	Name	Count	Type	Full Name
1	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:154 , ILE A:204 , GLN A:205 , LEU A:206 , SER A:207 , ASN A:211 , VAL A:285	BINDING SITE FOR RESIDUE MES A 1
2	AC2	SOFTWARE	ARG A:142 , ILE A:259 , PRO A:276	BINDING SITE FOR RESIDUE MPD A 341
3	AC3	SOFTWARE	GLU B:154 , ILE B:204 , GLN B:205 , LEU B:206 , SER B:207 , ASN B:211 , VAL B:285	BINDING SITE FOR RESIDUE MES B 2
4	AC4	SOFTWARE	HOH B:9 , THR B:139 , ARG B:142 , ILE B:259	BINDING SITE FOR RESIDUE MPD B 341

Asymmetric Unit

No.	Residues
1	A:110	-	A:172
2	A:184	-	A:192
3	A:291	-	A:323
4	B:110	-	B:172
5	B:184	-	B:192
6	B:291	-	B:323

(no "Cis Peptide Bond" information available for 3IWR)

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

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.	CHI2_ORYSJ	110-132	2	A:110-132 B:110-132
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHI2_ORYSJ	236-246	2	A:236-246 B:236-246

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.	CHI2_ORYSJ	110-132	1	A:110-132 -
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHI2_ORYSJ	236-246	1	A:236-246 -

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.	CHI2_ORYSJ	110-132	1	- B:110-132
2	CHITINASE_19_2	PS00774	Chitinases family 19 signature 2.	CHI2_ORYSJ	236-246	1	- B:236-246

(no "Exon" information available for 3IWR)

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:244
 aligned with CHI2_ORYSJ | Q7DNA1 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:244
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326    
           CHI2_ORYSJ    87 DGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
               SCOP domains d3iwra_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3iwrA01 A:87-174,A:233-330  [code=1.10.530.10, no name defined]                         3iwrA02 A:175-232 Endochitinase, domain 2                 3iwrA01 A:87-174,A:233-330  [code=1.10.530.10, no name defined]                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iwr A  87 DGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326

Chain B from PDB  Type:PROTEIN  Length:246
 aligned with CHI2_ORYSJ | Q7DNA1 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:246
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324      
           CHI2_ORYSJ    85 PSDGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
               SCOP domains d3iwrb_ B: automated matches                                                                                                                                                                                                                           SCOP domains
               CATH domains 3iwrB01 B:85-174,B:233-330  [code=1.10.530.10, no name defined]                           3iwrB02 B:175-232 Endochitinase, domain 2                 3iwrB01 B:85-174,B:233-330  [code=1.10.530.10, no name defined]                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3iwr B  85 PSDGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324

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(

)

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)

Oryza sativa [TaxId: 39947] (1)

1a	d3iwra_	A:
1b	d3iwrb_	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)

Japanese rice (Oryza sativa japonica group) (1)

1a	3iwrA02	A:175-232
1b	3iwrB02	B:175-232

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Japanese rice (Oryza sativa japonica group) (1)

2a	3iwrA01	A:87-174,A:233-330
2b	3iwrB01	B:85-174,B:233-330

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHI2_ORYSJ | Q7DNA1)

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:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	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.

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	CHI2_ORYSJ \| Q7DNA1	:	2dkv

2dkv	THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (6, 6)

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