3SCW - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RICE BGLU1 E386G/Y341A MUTANT COMPLEXED WITH CELLOTETRAOSE

Authors :   S. Pengthaisong, S. G. Withers, B. Kuaprasert, J. R. Ketudat Cairns

Date :   08 Jun 11 (Deposition) - 15 Feb 12 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

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

Reference :   S. Pengthaisong, S. G. Withers, B. Kuaprasert, J. R. Ketudat Cairns
Structural Investigation Of The Basis For Cellooligosaccharide Synthesis By Rice Bglu1 Glycosynthases
To Be Published
PubMed: search

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, 8)

No.	Name	Count	Type	Full Name
1	CTT	3	Ligand/Ion	BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-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, 4)

No.	Name	Count	Type	Full Name
1	CTT	2	Ligand/Ion	BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-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	CTT	1	Ligand/Ion	BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL-(1->4)-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 (8, 8)

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:606 , HOH A:696	BINDING SITE FOR RESIDUE SO4 A 1003
3	AC3	SOFTWARE	GLY A:278 , HIS A:279 , TYR A:280 , GLN A:285 , LYS A:294 , PHE A:295 , ALA A:300 , HOH A:796	BINDING SITE FOR RESIDUE MES A 1005
4	AC4	SOFTWARE	GLN A:29 , HIS A:130 , TYR A:131 , ASN A:175 , GLU A:176 , ILE A:179 , LEU A:182 , LEU A:183 , GLN A:187 , ASN A:245 , ASN A:313 , TYR A:315 , TRP A:358 , TRP A:433 , GLU A:440 , TRP A:441 , PHE A:449 , HOH A:556 , HOH A:596 , HOH A:639 , HOH A:640 , HOH A:665 , HOH A:710 , HOH A:732 , HOH A:774 , HOH A:789 , HOH A:826 , HOH A:829 , HOH A:896 , HOH A:898 , HOH A:912 , HOH A:920	BINDING SITE FOR RESIDUE CTT A 477
5	AC5	SOFTWARE	ASN A:5 , TRP A:6 , THR A:50 , PRO A:51 , ARG A:194 , ALA A:199 , ALA A:200 , GLY A:201 , TYR A:468 , ASP A:472 , HOH A:525 , HOH A:578 , HOH A:712 , HOH A:788 , HOH A:897 , HOH A:905	BINDING SITE FOR RESIDUE CTT A 478
6	AC6	SOFTWARE	THR B:163 , ASN B:166 , ARG B:167 , HOH B:591 , HOH B:907	BINDING SITE FOR RESIDUE SO4 B 1004
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:689	BINDING SITE FOR RESIDUE MES B 1006
8	AC8	SOFTWARE	GLN B:29 , HIS B:130 , TYR B:131 , ASN B:175 , GLU B:176 , ILE B:179 , LEU B:182 , LEU B:183 , GLN B:187 , ASN B:245 , ASN B:313 , TYR B:315 , TRP B:358 , TRP B:433 , GLU B:440 , TRP B:441 , PHE B:449 , HOH B:497 , HOH B:516 , HOH B:571 , HOH B:607 , HOH B:686 , HOH B:741 , HOH B:759 , HOH B:777 , HOH B:787 , HOH B:813 , HOH B:827 , HOH B:895 , HOH B:897 , HOH B:899 , HOH B:913	BINDING SITE FOR RESIDUE CTT B 1002

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 3SCW)

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

(no "Exon" information available for 3SCW)

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:472
 aligned with BGL07_ORYSJ | Q75I93 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:472
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  
          BGL07_ORYSJ    33 NWLGGLSRAAFPKRFVFGTATSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 504
               SCOP domains d3scwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3scw A   5 NWLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTAVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITGNGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 476
                                    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

Chain B from PDB  Type:PROTEIN  Length:472
 aligned with BGL07_ORYSJ | Q75I93 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:472
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502  
          BGL07_ORYSJ    33 NWLGGLSRAAFPKRFVFGTATSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTYVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITENGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 504
               SCOP domains d3scwb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....eeeee.hhhhhh..........hhhhhhhh....hhhhh......hhhhhhhhhhhhhhhh...eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeee..........hhhhhh..eee.ee..ee.............hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3scw B   5 NWLGGLSRAAFPKRFVFGTVTSAYQVEGMAASGGRGPSIWDAFAHTPGNVAGNQNGDVATDQYHRYKEDVNLMKSLNFDAYRFSISWSRIFPDGEGRVNQEGVAYYNNLINYLLQKGITPYVNLYHYDLPLALEKKYGGWLNAKMADLFTEYADFCFKTFGNRVKHWFTFNEPRIVALLGYDQGTNPPKRCTKCAAGGNSATEPYIVAHNFLLSHAAAVARYRTKYQAAQQGKVGIVLDFNWYEALSNSTEDQAAAQRARDFHIGWYLDPLINGHYPQIMQDLVKDRLPKFTPEQARLVKGSADYIGINQYTASYMKGQQLMQQTPTSYSADWQVTAVFAKNGKPIGPQANSNWLYIVPWGMYGCVNYIKQKYGNPTVVITGNGMDQPANLSRDQYLRDTTRVHFYRSYLTQLKKAIDEGANVAGYFAWSLLDNFEWLSGYTSKFGIVYVDFNTLERHPKASAYWFRDMLKH 476
                                    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

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	d3scwa_	A:
1b	d3scwb_	B:

(no "CATH Domain" information available for 3SCW)

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

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
		CTT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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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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	3scw
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	3.2.1.21
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2rgl	RICE BGLU1 BETA-GLUCOSIDASE, A PLANT EXOGLUCANASE BETA- GLUCOSIDASE.
2rgm	RICE BGLU1 BETA-GLUCOSIDASE COMPLEXED WITH 2-DEOXY-2- FLUOROGLUCOSIDE.
3aht	SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1 COMPLEXED WITH LAMINARIBIOSE.
3f4v	SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1, A PLANT EXOGLUCANASE BETA-GLUCOSIDASE.
3f5i	SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1 COMPLEXED WITH 2- DEOXY-2-FLUOROGLUCOSIDE.
3f5j	SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1 COMPLEXED WITH CELLOTETRAOSE.
3f5k	SEMI-ACTIVE E176Q MUTANT OF RICE BGLU1 COMPLEXED WITH CELLOPENTAOSE.
3scn
3sco
3scp
3scq
3scr
3scs
3sct
3scu
3scv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (19, 19)

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Related Entries

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Related Entries Specified in the PDB File