2J4G - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH N-BUTYL-THIAZOLINE INHIBITOR

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

Date :   31 Aug 06 (Deposition) - 30 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

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

Reference :   G. E. Whitworth, M. S. Macauley, K. A. Stubbs, R. J. Dennis, E. J. Taylor, G. J. Davies, I. R. Greig, D. J. Vocadlo
Analysis Of Pugnac And Nag-Thiazoline As Transition State Analogues For Human O-Glcnacase: Mechanistic And Structural Insights Into Inhibitor Selectivity And Transition State Poise.
J. Am. Chem. Soc. V. 129 635 2007
PubMed-ID: 17227027 | Reference-DOI: 10.1021/JA065697O
(for further references see the PDB file header)

Molecule 1 - HYALURONOGLUCOSAMINIDASE
	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	:	N-BUTYL-THIAZOLINE
	Strain	:	VPI-5482
	Synonym	:	O-GLCNACASE

		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 (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	NB1	2	Ligand/Ion	(3AR,5R,6S,7R,7AR)-5-(HYDROXYMETHYL)-2-PROPYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	NB1	1	Ligand/Ion	(3AR,5R,6S,7R,7AR)-5-(HYDROXYMETHYL)-2-PROPYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	NB1	1	Ligand/Ion	(3AR,5R,6S,7R,7AR)-5-(HYDROXYMETHYL)-2-PROPYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:562	BINDING SITE FOR RESIDUE ACT A1591
2	AC2	SOFTWARE	ASN A:288 , ASN A:290 , ASP B:243 , HIS B:433 , NB1 B:1590	BINDING SITE FOR RESIDUE ACT B1591
3	AC3	SOFTWARE	GLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , CYS A:278 , TYR A:282 , THR A:310 , TRP A:337 , ASN A:339 , ASP A:344 , TYR A:345 , ASN A:372	BINDING SITE FOR RESIDUE NB1 A1590
4	AC4	SOFTWARE	GLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , CYS B:278 , TYR B:282 , THR B:310 , TRP B:337 , ASN B:339 , ASP B:344 , TYR B:345 , ASN B:372 , ACT B:1591	BINDING SITE FOR RESIDUE NB1 B1590
5	AC5	SOFTWARE	TYR A:137 , ASP A:344 , TYR A:345 , ARG A:347 , GLN A:551 , ASN B:290	BINDING SITE FOR RESIDUE GOL A1719
6	AC6	SOFTWARE	ASN A:290 , TYR B:137 , ASP B:344 , TYR B:345 , ARG B:347 , GLN B:551	BINDING SITE FOR RESIDUE GOL B1719

(no "SS Bond" information available for 2J4G)

Asymmetric Unit

No.	Residues
1	Gln A:6	-	Pro A:7
2	Gly A:47	-	Lys A:48
3	Lys A:53	-	Gly A:54
4	Ala A:173	-	Pro A:174
5	Phe A:340	-	Pro A:341
6	Gln B:6	-	Pro B:7
7	Gly B:47	-	Lys B:48
8	Ala B:173	-	Pro B:174
9	Gly B:291	-	Asn B:292
10	Phe B:340	-	Pro B:341

(no "SAP(SNP)/Variant" information available for 2J4G)

(no "PROSITE Motif" information available for 2J4G)

(no "Exon" information available for 2J4G)

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:586
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:586
                                    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      
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 610
               SCOP domains d2j4ga3 A:4-126 Glucosaminidase GH84, N-terminal domain                                                                    d2j4ga2 A:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2j4ga1 A:437-589 Glucosaminidase GH84 post-catalytic domain                                                                                              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.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4g A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 589
                                    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

Chain B from PDB  Type:PROTEIN  Length:580
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:586
                                    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      
            OGA_BACTN    25 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 610
               SCOP domains d2j4gb3 B:4-126 Glucosaminidase GH84, N-termina   l domain                                                                 d2j4gb2 B:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2j4gb1 B:437-589   Glucosaminidase GH84 post-catalytic domain                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee....eeee.....hhhhhhhhhhhh...ee---eeeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee.....hhhh-...hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee...........................eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...............hhhhhhhhhhhhhh.--....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j4g B   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQS---GMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWS-PNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAF--GKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTD 589
                                    13        23        33        43      |  -|       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      
                                                                         50  54                                                                                                                                                                                                                                      287 |                                                                                                                                                                  454  |                                                                                                                                    
                                                                                                                                                                                                                                                                                                                       289                                                                                                                                                                     457

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 2J4G)

(no "Pfam Domain" information available for 2J4G)

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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	Ligands, Modified Residues, Ions
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		AC6	[ RasMol ]	+environment [ RasMol ]

	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 ]
		Gly A:47 - Lys A:48	[ RasMol ]
		Gly B:291 - Asn B:292	[ RasMol ]
		Gly B:47 - Lys B:48	[ RasMol ]
		Lys A:53 - Gly A:54	[ RasMol ]
		Phe A:340 - Pro A:341	[ RasMol ]
		Phe B:340 - Pro B:341	[ RasMol ]

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	2j4g
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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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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