2RGL - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   RICE BGLU1 BETA-GLUCOSIDASE, A PLANT EXOGLUCANASE/BETA-GLUCOSIDASE

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

Date :   04 Oct 07 (Deposition) - 12 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

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

Reference :   W. Chuenchor, S. Pengthaisong, R. C. Robinson, J. Yuvaniyama, W. Oonanant, D. R. Bevan, A. Esen, C. J. Chen, R. Opassiri, J. Svasti, J. R. K. Cairns
Structural Insights Into Rice Bglu1 Beta-Glucosidase Oligosaccharide Hydrolysis And Transglycosylation
J. Mol. Biol. V. 377 1200 2008
PubMed-ID: 18308333 | Reference-DOI: 10.1016/J.JMB.2008.01.076

Molecule 1 - BETA-GLUCOSIDASE
	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
	Fragment	:	RESIDUES UNP 29-504
	Gene	:	OS3BGLU7
	Organism Scientific	:	ORYZA SATIVA JAPONICA GROUP
	Organism Taxid	:	39947
	Strain	:	ORION

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
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	GOL	1	Ligand/Ion	GLYCEROL
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	GOL	1	Ligand/Ion	GLYCEROL
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 3 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:65 , HIS A:68 , ASP B:65 , HIS B:68	BINDING SITE FOR RESIDUE ZN A 1001
2	AC2	SOFTWARE	THR A:163 , ASN A:166 , ARG A:167 , HOH A:1047 , HOH A:1216	BINDING SITE FOR RESIDUE SO4 A 1002
3	AC3	SOFTWARE	THR B:163 , ASN B:166 , ARG B:167 , HOH B:1047 , HOH B:1479 , HOH B:1565	BINDING SITE FOR RESIDUE SO4 B 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 , HOH A:1069 , HOH A:1300	BINDING SITE FOR RESIDUE MES A 1003
5	AC5	SOFTWARE	GLY B:278 , HIS B:279 , TYR B:280 , GLN B:285 , LYS B:294 , PHE B:295 , ALA B:300 , HOH B:1098 , HOH B:1310	BINDING SITE FOR RESIDUE MES B 1003
6	AC6	SOFTWARE	GLN A:29 , GLU A:176 , TYR A:315 , GLU A:386 , TRP A:433 , GLU A:440 , TRP A:441 , PHE A:449 , HOH A:1072 , HOH A:1184 , HOH A:1353	BINDING SITE FOR RESIDUE GOL A 1004
7	AC7	SOFTWARE	GLN B:29 , GLU B:176 , TYR B:315 , GLU B:386 , TRP B:433 , GLU B:440 , TRP B:441 , PHE B:449 , HOH B:1529 , HOH B:1530	BINDING SITE FOR RESIDUE GOL B 1004

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 2RGL)

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

(no "Exon" information available for 2RGL)

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 d2rgla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2rglA00 A: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..........hhhhhh..eee.ee..ee.............hhhhhhhhhhhhhhh....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.ee...eee......eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgl A   6 WLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 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 d2rglb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2rglB00 B:6-476 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) -----Glyco_hydro_1-2rglB01 B:11-476                                                                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains (1)
           Pfam domains (2) -----Glyco_hydro_1-2rglB02 B:11-476                                                                                                                                                                                                                                                                                                                                                                                                                                                     Pfam domains (2)
         Sec.struct. author .....hhhhh....eeeee.hhhhhh..........hhhhhhhh....hhhhh......hhhhhhhhhhhhhhhh...eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeee..........hhhhhh..eee.ee..ee.............hhhhhhhhhhhhhhh....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.ee...eee......eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgl B   6 WLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 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	d2rgla_	A:
1b	d2rglb_	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)

Oryza sativa japonica group. Organism_taxid: 39947. Strain: orion. (2)

1a	2rglA00	A:6-476
1b	2rglB00	B:6-476

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_1 (36)

Oryza sativa subsp. japonica (Rice) (2)

1a	Glyco_hydro_1-2rglB01	B:11-476
1b	Glyco_hydro_1-2rglB02	B:11-476

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
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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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