3AHT - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RICE BGLU1 E176Q MUTANT IN COMPLEX WITH LAMINARIBIOSE

Authors :   W. Chuenchor, S. Pengthaisong, R. C. Robinson, J. Yuvaniyama, J. Svast J. R. Ketudat Cairns

Date :   29 Apr 10 (Deposition) - 02 Jun 10 (Release) - 22 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Beta-Alpha-Barrels, Glycoside Hydrolase, Oligosaccharide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Chuenchor, S. Pengthaisong, R. C. Robinson, J. Yuvaniyama, J. Svasti, J. R. Ketudat Cairns
The Structural Basis Of Oligosaccharide Binding By Rice Bglu1 Beta-Glucosidase
J. Struct. Biol. V. 173 169 2011
PubMed-ID: 20884352 | Reference-DOI: 10.1016/J.JSB.2010.09.021

Molecule 1 - BETA-GLUCOSIDASE 7
	Chains	:	A, B
	EC Number	:	3.2.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32A
	Expression System Strain	:	ORIGAMI(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BGLU1, BGLU7, LOC_OS03G49600, OS03G0703000, OS3BGLU7, OSJNBA0004L11.16
	Mutation	:	YES
	Organism Common	:	JAPANESE RICE
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Strain	:	ORION
	Synonym	:	OS3BGLU7

		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 (4, 7)

No.	Name	Count	Type	Full Name
1	LB2	2	Ligand/Ion	3-O-BETA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	LB2	1	Ligand/Ion	3-O-BETA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	LB2	1	Ligand/Ion	3-O-BETA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSE
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:29 , HIS A:130 , ASN A:175 , GLN A:176 , ASN A:245 , ASN A:313 , TYR A:315 , TRP A:358 , GLU A:386 , TRP A:433 , GLU A:440 , TRP A:441 , PHE A:449	BINDING SITE FOR RESIDUE LB2 A 1000
2	AC2	SOFTWARE	ASP A:65 , HIS A:68 , ASP B:65 , HIS B:68	BINDING SITE FOR RESIDUE ZN A 1001
3	AC3	SOFTWARE	ASN A:166 , ARG A:167	BINDING SITE FOR RESIDUE SO4 A 1002
4	AC4	SOFTWARE	GLY A:278 , HIS A:279 , TYR A:280 , GLN A:285 , LYS A:294 , PHE A:295 , ALA A:300	BINDING SITE FOR RESIDUE MES A 1003
5	AC5	SOFTWARE	GLN B:29 , HIS B:130 , ASN B:175 , GLN B:176 , ASN B:245 , ASN B:313 , TYR B:315 , TRP B:358 , GLU B:386 , TRP B:433 , GLU B:440 , TRP B:441 , PHE B:449	BINDING SITE FOR RESIDUE LB2 B 1000
6	AC6	SOFTWARE	ASN B:166 , ARG B:167	BINDING SITE FOR RESIDUE SO4 B 1002
7	AC7	SOFTWARE	GLY B:278 , HIS B:279 , TYR B:280 , GLN B:285 , LYS B:294 , PHE B:295 , ALA B:300 , HOH B:508	BINDING SITE FOR RESIDUE MES B 1003

Asymmetric Unit

No.	Residues
1	A:195	-	A:198
2	B:195	-	B:198

Asymmetric Unit

No.	Residues
1	Pro A:191	-	Pro A:192
2	Trp A:433	-	Ser A:434
3	Pro B:191	-	Pro B:192
4	Trp B:433	-	Ser B:434

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

(no "PROSITE Motif" information available for 3AHT)

(no "Exon" information available for 3AHT)

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:471
 aligned with BGL07_ORYSJ | Q75I93 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:471
                                    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 
          BGL07_ORYSJ    34 WLGGLSRAAFPKRFVFGTATSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 504
               SCOP domains d3ahta_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3ahtA00 A:6-476 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeee.hhhhhh..........hhhhhhhhh...hhhhh......hhhhhhhhhhhhhhhh...eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeee............hhhhh.eee.ee..ee.............hhhhhhhhhhhhhhh....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh..ee...eee......eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aht A   6 WLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNQPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 476
                                    15        25        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

Chain B from PDB  Type:PROTEIN  Length:471
 aligned with BGL07_ORYSJ | Q75I93 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:471
                                    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 
          BGL07_ORYSJ    34 WLGGLSRAAFPKRFVFGTATSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 504
               SCOP domains d3ahtb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3ahtB00 B:6-476 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh....eeeee.hhhhhh..........hhhhhhhh....hhhhh......hhhhhhhhhhhhhhhh...eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeee............hhhhh.eee.ee..ee.............hhhhhhhhhhhhhhh....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhh..ee...eee......eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aht B   6 WLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNQPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 476
                                    15        25        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

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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: automated matches (180)

Protein domain: automated matches (180)

Oryza sativa [TaxId: 39947] (23)

1a	d3ahta_	A:
1b	d3ahtb_	B:

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)

Japanese rice (Oryza sativa japonica group) (6)

1a	3ahtA00	A:6-476
1b	3ahtB00	B:6-476

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BGL07_ORYSJ | Q75I93)

molecular function
	GO:0047668	amygdalin beta-glucosidase activity	Catalysis of the reaction: (R)-amygdalin + H(2)O = (R)-prunasin + D-glucose.
	GO:0033907	beta-D-fucosidase activity	Catalysis of the hydrolysis of terminal non-reducing beta-D-fucose residues in beta-D-fucosides.
	GO:0047701	beta-L-arabinosidase activity	Catalysis of the reaction: H2O + a beta-L-arabinoside = L-arabinose + an alcohol.
	GO:0004565	beta-galactosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
	GO:0080083	beta-gentiobiose beta-glucosidase activity	Catalysis of the hydrolysis of glucosidic link in beta-gentiobiose.
	GO:0008422	beta-glucosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
	GO:0004567	beta-mannosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides.
	GO:0080079	cellobiose glucosidase activity	Catalysis of the reaction: cellobiose + H2O = 2 D-glucose.
	GO:0042973	glucan endo-1,3-beta-D-glucosidase activity	Catalysis of the hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
	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.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0050224	prunasin beta-glucosidase activity	Catalysis of the reaction: (R)-prunasin + H(2)O = D-glucose + mandelonitrile.
	GO:0102483	scopolin beta-glucosidase activity	Catalysis of the reaction: H2O + scopolin <=> beta-D-glucose + scopoletin
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:1901657	glycosyl compound metabolic process	The chemical reactions and pathways involving glycosyl compound.
	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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Pro A:191 - Pro A:192	[ RasMol ]
		Pro B:191 - Pro B:192	[ RasMol ]
		Trp A:433 - Ser A:434	[ RasMol ]
		Trp B:433 - Ser B:434	[ RasMol ]

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2rgl	APOENZYME OF RICE BGLU1 WILDTYPE PROTEIN
3ahv	COVALENT COMPLEX OF RICE BGLU1 E176Q WITH 2-DEOXY-2- FLUOROGLUCOSIDE
3f4v	APO ENZYME FOR RICE BGLU1 E176Q MUTANT
3f5j	COMPLEX OF RICE BGLU1 E176Q MUTANT WITH CELLOTETRAOSE
3f5k	COMPLEX OF RICE BGLU1 176Q MUTANT WITH CELLOPENTAOSE
3f5l	PREVIOUS LAMINARIBIOSE COMPLEX WITH HIGH RESOLUTION, BUT VERY LOW OCCUPANCY OF THE LIGAND.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (19, 19)

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Related Entries Specified in the PDB File