1K9T - JenaLib

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Title :   CHITINASE A COMPLEXED WITH TETRA-N-ACETYLCHITOTRIOSE

Authors :   G. Prag, P. A. Tucker, A. B. Oppenheim

Date :   30 Oct 01 (Deposition) - 06 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Glycosyl Hydrolase Family 18, Chitinase, Chitinolysis, A/B-(Tim)- Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Prag, P. A. Tucker, A. B. Oppenheim
Complex Structures Of Chitinase A Mutant With Oligonag Provide Insight Into The Enzymatic Mechanism
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - CHITINASE A
	Chains	:	A
	EC Number	:	3.2.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-3
	Expression System Strain	:	A9588
	Expression System Vector Type	:	PLASMID
	Gene	:	CHIA
	Mutation	:	YES
	Organism Scientific	:	SERRATIA MARCESCENS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	NAG A:7 , TYR A:163 , PHE A:191 , GLY A:274 , TRP A:275 , ASP A:313 , GLU A:315 , MET A:388 , TYR A:390 , TYR A:444 , ARG A:446 , TRP A:539 , HOH A:924 , HOH A:1005	BINDING SITE FOR RESIDUE NAG A 6
2	AC2	SOFTWARE	NAG A:6 , NAG A:8 , TRP A:275 , GLU A:315 , PHE A:316 , MET A:388 , ARG A:446 , HOH A:647 , HOH A:935 , HOH A:1234	BINDING SITE FOR RESIDUE NAG A 7
3	AC3	SOFTWARE	NAG A:7 , NAG A:9 , TRP A:275 , LYS A:369 , ALA A:391 , PHE A:396 , TYR A:418 , HOH A:953 , HOH A:1142 , HOH A:1269	BINDING SITE FOR RESIDUE NAG A 8
4	AC4	SOFTWARE	NAG A:8 , PHE A:392 , PHE A:396 , ASP A:397 , TYR A:418 , HOH A:909 , HOH A:1058	BINDING SITE FOR RESIDUE NAG A 9

Asymmetric Unit

No.	Residues
1	A:115	-	A:120
2	A:195	-	A:218

Asymmetric Unit

No.	Residues
1	Gly A:190	-	Phe A:191
2	Glu A:315	-	Phe A:316
3	Trp A:539	-	Glu A:540

(no "SAP(SNP)/Variant" information available for 1K9T)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIA_SERMA	307-315	1	A:307-315

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHITINASE_18	PS01095	Chitinases family 18 active site.	CHIA_SERMA	307-315	2	A:307-315

(no "Exon" information available for 1K9T)

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:538
 aligned with CHIA_SERMA | P07254 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:538
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553        
           CHIA_SERMA    24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDAGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGPFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKVVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWKNGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
               SCOP domains d1k9ta1 A:24-132 Chitinase A, N-terminal domain N                                                            d1k9ta2 A:133-443,A:517-561 Chitinase A, catalytic domain                                                                                                                                                                                                                                                              d1k9ta3 A:444-516 Chitinase A                                            d1k9ta2 A:133-443,A:517-561                   SCOP domains
               CATH domains 1k9tA01 A:24-130 Immunoglobulins                                                                           1k9tA02 A:131-442,A:519-561 Glycosidases                                                                                                                                                                                                                                                                                1k9tA03 A:443-518  [code=3.10.50.10, no name defined]                       1k9tA02 A:131-442,A:519-561 Glycosidases    CATH domains
               Pfam domains ChitinaseA_N-1k9tA01 A:24-156                                                                                                        -Glyco_hydro_18-1k9tA02 A:158-544                                                                                                                                                                                                                                                                                                                                                                   ----------------- Pfam domains
         Sec.struct. author ......ee.....eee.eee.....hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee....................ee.....eeeeeee.hhhh....hhhhhhhhhh.eeeeeee........hhhhhhh.hhhhhhhhhh...........hhhhhhh.............hhhhhhhhhhhhhh...eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................hhhhhhhhhhhhh.hhh.eeeeee.eeeeee........hhhhh...ee........eeehhhhhhhh.....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k9t A  24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKVLLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSVETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYAFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553

Chain A from PDB  Type:PROTEIN  Length:538
 aligned with O83008_SERMA | O83008 from UniProtKB/TrEMBL  Length:563

    Alignment length:538
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553        
         O83008_SERMA    24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKVLLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSVETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENRIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
               SCOP domains d1k9ta1 A:24-132 Chitinase A, N-terminal domain N                                                            d1k9ta2 A:133-443,A:517-561 Chitinase A, catalytic domain                                                                                                                                                                                                                                                              d1k9ta3 A:444-516 Chitinase A                                            d1k9ta2 A:133-443,A:517-561                   SCOP domains
               CATH domains 1k9tA01 A:24-130 Immunoglobulins                                                                           1k9tA02 A:131-442,A:519-561 Glycosidases                                                                                                                                                                                                                                                                                1k9tA03 A:443-518  [code=3.10.50.10, no name defined]                       1k9tA02 A:131-442,A:519-561 Glycosidases    CATH domains
               Pfam domains ChitinaseA_N-1k9tA01 A:24-156                                                                                                        -Glyco_hydro_18-1k9tA02 A:158-544                                                                                                                                                                                                                                                                                                                                                                   ----------------- Pfam domains
         Sec.struct. author ......ee.....eee.eee.....hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee....................ee.....eeeeeee.hhhh....hhhhhhhhhh.eeeeeee........hhhhhhh.hhhhhhhhhh...........hhhhhhh.............hhhhhhhhhhhhhh...eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................hhhhhhhhhhhhh.hhh.eeeeee.eeeeee........hhhhh...ee........eeehhhhhhhh.....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k9t A  24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKVLLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSVETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYAFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Serratia marcescens. (1)

1k9tA02

A:131-442,A:519-561

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.10, no name defined] (121)

Serratia marcescens. (1)

1k9tA03

A:443-518

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Serratia marcescens. (1)

1k9tA01

A:24-130

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: E-set (290)

Family: ChitinaseA_N (9)

Serratia marcescens (9)

ChitinaseA_N-1k9tA01

A:24-156

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_18 (72)

Serratia marcescens (17)

Glyco_hydro_18-1k9tA02

A:158-544

Asymmetric Unit(hide GO term definitions)

Chain A (O83008_SERMA | O83008)

molecular function
	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.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-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: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: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.

Chain A (CHIA_SERMA | P07254)

molecular function
	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.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-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: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: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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:315 - Phe A:316	[ RasMol ]
		Gly A:190 - Phe A:191	[ RasMol ]
		Trp A:539 - Glu A:540	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1k9t
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	O83008_SERMA \| O83008
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	3.2.1.14
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UniProtKB/Swiss-Prot
	CHIA_SERMA \| P07254	:	1ctn 1ehn 1eib 1ffq 1ffr 1nh6 1rd6 1x6l 1x6n 2wk2 2wly 2wlz 2wm0
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	O83008_SERMA \| O83008	:	1edq

1ctn	1CTN CONTAINS A BACTERIAL CHITINASE AT 2.3 A RESOLUTION.
1ehn	1EHN CONTAINS CHITINASE A MUTANT E315Q COMPLEXED WITH OCTA- N-ACETYLCHITOOCTAOSE (NAG)8.
1eib	1EIB CONTAINS CHITINASE A MUTANT D313A COMPLEXED WITH OCTA- N-ACETYLCHITOOCTAOSE (NAG)8.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (3, 3)

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