2W67 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   BTGH84 IN COMPLEX WITH FMA34

Authors :   Y. He, G. J. Davies

Date :   17 Dec 08 (Deposition) - 14 Apr 09 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

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

Keywords :   Glycoside Hydrolase, Complex, Hydrolase, Inhibitor, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Marcelo, Y. He, S. A. Yuzwa, L. Nieto, J. Jimenez-Barbero, M. Sollogoub, D. J. Vocadlo, G. J. Davies, Y. Bleriot
Molecular Basis For Inhibition Of Gh84 Glycoside Hydrolases By Substituted Azepanes: Conformational Flexibility Enables Probing Of Substrate Distortion.
J. Am. Chem. Soc. V. 131 5390 2009
PubMed-ID: 19331390 | Reference-DOI: 10.1021/JA809776R

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	:	YSBLLICPET28
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON VPI-5482
	Organism Taxid	:	226186
	Synonym	:	BTGH84, BETA-HEXOSAMINIDASE, N-ACETYL-BETA-GLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, HEXOSAMINIDASE B, GH84

		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, 5)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	F34	2	Ligand/Ion	N-[(3S,4R,5R,6R)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	F34	1	Ligand/Ion	N-[(3S,4R,5R,6R)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	F34	1	Ligand/Ion	N-[(3S,4R,5R,6R)-4,5,6-TRIHYDROXYAZEPAN-3-YL]ACETAMIDE
3	GOL	-1	Ligand/Ion	GLYCEROL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:135 , PHE A:136 , LYS A:166 , ASP A:242 , ASP A:243 , TYR A:282 , VAL A:314 , ASN A:339 , VAL A:342 , ASP A:344 , ASN A:372 , HOH A:2283	BINDING SITE FOR RESIDUE F34 A1716
2	AC2	SOFTWARE	GLY B:135 , PHE B:136 , LYS B:166 , ASP B:242 , ASP B:243 , TYR B:282 , VAL B:314 , ASN B:339 , VAL B:342 , ASP B:344 , ASN B:372 , HOH B:2240	BINDING SITE FOR RESIDUE F34 B1589
3	AC3	SOFTWARE	LEU A:178 , PRO A:354 , TYR A:356 , TRP A:400 , GLU A:438 , HOH A:2213 , HOH A:2284 , HOH A:2285	BINDING SITE FOR RESIDUE GOL A1717
4	AC4	SOFTWARE	GLU A:32 , GLU A:61 , ASP A:64	BINDING SITE FOR RESIDUE CA A1718
5	AC5	SOFTWARE	GLU B:32 , GLU B:61 , ASP B:64	BINDING SITE FOR RESIDUE CA B1590

(no "SS Bond" information available for 2W67)

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	Gln B:6	-	Pro B:7
5	Ala B:173	-	Pro B:174
6	Phe B:340	-	Pro B:341

(no "SAP(SNP)/Variant" information available for 2W67)

(no "PROSITE Motif" information available for 2W67)

(no "Exon" information available for 2W67)

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:642
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:711
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735 
            OGA_BACTN    26 LQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGKDAPCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEK 736
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee--eeeeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee.hhhhh..hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...............hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh...............--------...eeee..eeee..------------.eeeeeeeeeeeeeee..----------------------------------.....eeeeee.-------------.eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w67 A   5 LQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQS--KGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKM--------NLPLQVKANRVLISP------------VEIELDAIYPGENIQINF----------------------------------GLQKAPVKFVRF-------------QFVLTIEK 715
                                    14        24        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   |     -      |634       644   |     -         -         -       684       694         -   |   714 
                                                                        50 53                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           595      604           618          631              648                                683        694           708

Chain B from PDB  Type:PROTEIN  Length:576
 aligned with OGA_BACTN | Q89ZI2 from UniProtKB/Swiss-Prot  Length:737

    Alignment length:584
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605    
            OGA_BACTN    26 LQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATT 609
               SCOP domains d2w67b1 B:5-126 Glucosaminidase GH84, N-t        erminal domain                                                           d2w67b2 B:127-436 Glucosaminidase GH84, catalytic domain                                                                                                                                                                                                                                                              d2w67b3 B:437-588 Glucosaminidase GH84 post-catalytic domain                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------Glyco_hydro_20b-2w67B03 B:65-125                             ----NAGidase-2w67B01 B:130-425                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------Glyco_hydro_20b-2w67B04 B:65-125                             ----NAGidase-2w67B02 B:130-425                                                                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeeeee....eeee.....hhhhhhhhhhh.--------.eeeeeee.....hhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w67 B   5 LQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELL--------GMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATT 588
                                    14        24        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    
                                                                   45       54

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 2W67)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: NAGidase (15)

Bacteroides thetaiotaomicron (10)

1a	NAGidase-2w67B01	B:130-425
1b	NAGidase-2w67B02	B:130-425

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

Family: Glyco_hydro_20b (22)

Bacteroides thetaiotaomicron (10)

2a	Glyco_hydro_20b-2w67B03	B:65-125
2b	Glyco_hydro_20b-2w67B04	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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	Ligands, Modified Residues, Ions
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		F34	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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 ]
		Phe A:340 - Pro A:341	[ RasMol ]
		Phe B:340 - Pro B:341	[ RasMol ]

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	2w67
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	OGA_BACTN \| Q89ZI2
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	3.2.1.52
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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
2jiw	BACTEROIDES THETAIOTAOMICRON GH84 O-GLCNACASE IN COMPLEX WITH 2-ACETYLAMINO-2-DEOXY-1- EPIVALIENAMINE
2vvn	BTGH84 IN COMPLEX WITH NH-BUTYLTHIAZOLINE
2vvs	BTGH84 STRUCTURE IN COMPLEX WITH PUGNAC
2vw3	BTGH84 IN COMPLEX WITH AMINO THIAZOLINE
2w4x	BTGH84 IN COMPLEX WITH STZ
2w66	BTGH84 IN COMPLEX WITH HQ602

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (2, 4)

Gene Ontology (7, 7)

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