2JIW - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH 2-ACETYLAMINO-2-DEOXY-1-EPIVALIENAMINE

Authors :   R. J. Dennis, G. J. Davies

Date :   02 Jul 07 (Deposition) - 07 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   O-Glcnacase, Glycosidase, Epivalienamine, Gh84, Enzyme, Hydrolase, Inhibitor, Inhibition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Scaffidi, K. A. Stubbs, R. J. Dennis, E. J. Taylor, G. J. Davies, D. J. Vocadlo, R. V. Stick
A 1-Acetamido Derivative Of 6-Epi-Valienamine: An Inhibitor Of A Diverse Group Of Beta-N- Acetylglucosaminidases.
Org. Biomol. Chem. V. 5 3013 2007
PubMed-ID: 17728868 | Reference-DOI: 10.1039/B709681J
(for further references see the PDB file header)

Molecule 1 - O-GLCNACASE BT_4395
	Atcc	:	29148
	Chains	:	A, B
	EC Number	:	3.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 23-737
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	226186
	Other Details	:	2-ACETYLAMINO-2-DEOXY-1-EPIVALIENAMINE
	Strain	:	VPI-5482
	Synonym	:	BETA-HEXOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, HEXOSAMINIDASE B, GH84, BETA-N-ACETYLGLUCOSAMINIDASE

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	BEU	2	Ligand/Ion	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BEU	1	Ligand/Ion	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BEU	1	Ligand/Ion	N-[(1S,2R,5R,6R)-2-AMINO-5,6-DIHYDROXY-4-(HYDROXYMETHYL)CYCLOHEX-3-EN-1-YL]ACETAMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:135 , PHE A:136 , LYS A:166 , ASP A:242 , ASP A:243 , CYS A:278 , TYR A:282 , THR A:310 , VAL A:314 , ILE A:315 , TRP A:337 , ASN A:339 , VAL A:342 , ASP A:344 , TYR A:345 , ASN A:372 , HOH A:2290 , HOH A:2362 , HOH A:2363	BINDING SITE FOR RESIDUE BEU A1594
2	AC2	SOFTWARE	GLY B:135 , PHE B:136 , LYS B:166 , ASP B:242 , ASP B:243 , CYS B:278 , TYR B:282 , THR B:310 , VAL B:314 , TRP B:337 , ASN B:339 , ASP B:344 , TYR B:345 , ASN B:372 , HOH B:2310 , HOH B:2402 , HOH B:2403	BINDING SITE FOR RESIDUE BEU B1594

(no "SS Bond" information available for 2JIW)

Asymmetric Unit

No.	Residues
1	Gln A:6	-	Pro A:7
2	Ala A:173	-	Pro A:174
3	Phe A:340	-	Pro A:341
4	Lys A:458	-	Asn A:459
5	Gln B:6	-	Pro B:7
6	Ala B:173	-	Pro B:174
7	Phe B:340	-	Pro B:341
8	Lys B:458	-	Asn B:459

(no "SAP(SNP)/Variant" information available for 2JIW)

(no "PROSITE Motif" information available for 2JIW)

(no "Exon" information available for 2JIW)

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:590
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:590
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPH 614
               SCOP domains d2jiwa3 A:4-126 automated matches                                                                                          d2jiwa2 A:127-436 automated matches                                                                                                                                                                                                                                                                                   d2jiwa1 A:437-593 automated matches                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee....eeee.....hhhhhhhhhhhh.........eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jiw A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPH 593
                                    13        23        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       563       573       583       593

Chain B from PDB  Type:PROTEIN  Length:590
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:590
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPH 614
               SCOP domains d2jiwb3 B:4-126 automated matches                                                                                          d2jiwb2 B:127-436 automated matches                                                                                                                                                                                                                                                                                   d2jiwb1 B:437-593 automated matches                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------Glyco_hydro_20b-2jiwB03 B:65-125                             ----NAGidase-2jiwB01 B:130-425                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------Glyco_hydro_20b-2jiwB04 B:65-125                             ----NAGidase-2jiwB02 B:130-425                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee....eeee.....hhhhhhhhhhhh.........eeeeeee.....hhhhhhhh......eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jiw B   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPH 593
                                    13        23        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       563       573       583       593

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 '\|'

(no "CATH Domain" information available for 2JIW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: NAGidase (15)

Bacteroides thetaiotaomicron (10)

1a	NAGidase-2jiwB01	B:130-425
1b	NAGidase-2jiwB02	B:130-425

Clan: no clan defined [family: Glyco_hydro_20b] (22)

Family: Glyco_hydro_20b (22)

Bacteroides thetaiotaomicron (10)

2a	Glyco_hydro_20b-2jiwB03	B:65-125
2b	Glyco_hydro_20b-2jiwB04	B:65-125

Asymmetric Unit(hide GO term definitions)

Chain A,B (OGA_BACTN | Q89ZI2)

molecular function
	GO:0016231	beta-N-acetylglucosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides.
	GO:0004563	beta-N-acetylhexosaminidase activity	Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
	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: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:0006517	protein deglycosylation	The removal of sugar residues from a glycosylated protein.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:173 - Pro A:174	[ RasMol ]
		Ala B:173 - Pro B:174	[ RasMol ]
		Gln A:6 - Pro A:7	[ RasMol ]
		Gln B:6 - Pro B:7	[ RasMol ]
		Lys A:458 - Asn A:459	[ RasMol ]
		Lys B:458 - Asn B:459	[ RasMol ]
		Phe A:340 - Pro A:341	[ RasMol ]
		Phe B:340 - Pro B:341	[ RasMol ]

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2chn	BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY
2cho	BACTEROIDES THETAIOTAOMICRON HEXOSAMINIDASE WITH O-GLCNACASE ACTIVITY
2j47	BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH A IMIDAZOLE-PUGNAC HYBRID INHIBITOR
2j4g	BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH N-BUTYL-THIAZOLINE INHIBITOR

Description

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Ligands, Modified Residues, Ions (1, 2)

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Cis Peptide Bonds (8, 8)

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