3AIV - JenaLib

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Asym. Unit - sites (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BETA-GLUCOSIDASE IN RYE COMPLEXED WITH AN AGLYCONE DIMBOA

Authors :   M. Sue, C. Nakamura, T. Miyamoto, S. Yajima

Date :   18 May 10 (Deposition) - 23 Feb 11 (Release) - 04 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)
Biol. Unit 2: A  (2x)

Keywords :   Tim Barrel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sue, C. Nakamura, T. Miyamoto, S. Yajima
Active-Site Architecture Of Benzoxazinone-Glucoside Beta-D-Glucosidases In Triticeae
Plant Sci. V. 180 268 2011
PubMed-ID: 21421370 | Reference-DOI: 10.1016/J.PLANTSCI.2010.09.001

Molecule 1 - BETA-GLUCOSIDASE
	Chains	:	A
	EC Number	:	3.2.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21 CODONPLUS(DE3) RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES IN UNP 50-568
	Gene	:	SCGLU
	Organism Common	:	RYE
	Organism Scientific	:	SECALE CEREALE
	Organism Taxid	:	4550

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	HBO	1	Ligand/Ion	2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	HBO	6	Ligand/Ion	2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HBO	2	Ligand/Ion	2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:191 , THR A:194 , PHE A:198 , TRP A:379 , GLU A:407 , GLU A:462 , HOH A:540 , HOH A:581 , HOH A:626 , HOH A:632	BINDING SITE FOR RESIDUE HBO A 900

Asymmetric Unit

No.	Residues
1	A:210	-	A:216

Asymmetric Unit

No.	Residues
1	Ala A:206	-	Pro A:207

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	HGGL_SECCE	82-96	1	A:33-47
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	HGGL_SECCE	452-460	1	A:403-411

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	HGGL_SECCE	82-96	6	A:33-47
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	HGGL_SECCE	452-460	6	A:403-411

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	HGGL_SECCE	82-96	2	A:33-47
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	HGGL_SECCE	452-460	2	A:403-411

(no "Exon" information available for 3AIV)

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:486
 aligned with HGGL_SECCE | Q9FYS3 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:486
                                    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       512       522       532       542      
           HGGL_SECCE    63 VFTKLKPWQIPKRDWFSKDFLFGASTSAYQIEGAWNEDGKGPSTWDHFCHTYPERISDGTNGDVAANSYHMYEEDVKALKDMGMKVYRFSISWSRILPNGTGKPNQKGIDYYNNLINSLIRHGIVPYVTIWHWDTPQALEDKYGGFLDKQIVNDYKYFAELCFQSFGDRVKNWFTFNEPHTYCCFSYGEGIHAPGRCSPGLDCAVPEGDSLREPYTAGHHILLAHAEAVELFKAHYNKHGDSKIGMAFDVMGYEPYQDSFLDDQARERSIDYNMGWFLEPVVRGDYPFSMRSLIGDRLPMFTKEEQEKLGSLCDIMGLNYYTSRFSKHVDISSDYTPTLNTDDAYASSETTGSDGNEIGPITGTYWIYMYPKGLTDLLLIMKEKYGNPPIFITENGIADVEGDPEMPDPLDDWKRLDYLQRHISAVKDAIDQGADVRGHFTWGLIDNFEWGSGYSSRFGLVYIDKEDGNKRKLKKSAKWFAKFNSV 548
               SCOP domains d3aiva_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh.......hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..........hhhhhh.eeee....................hhhhhhhhhhhhhhh.....eeeee....ee...........hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhhh.ee...eee.hhhh..eeehhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3aiv A  14 VFTKLKPWQIPKRDWFSKDFLFGASTSAYQIEGAWNEDGKGPSTWDHFCHTYPERISDGTNGDVAANSYHMYEEDVKALKDMGMKVYRFSISWSRILPNGTGKPNQKGIDYYNNLINSLIRHGIVPYVTIWHWDTPQALEDKYGGFLDKQIVNDYKYFAELCFQSFGDRVKNWFTFNEPHTYCCFSYGEGIHAPGRCSPGLDCAVPEGDSLREPYTAGHHILLAHAEAVELFKAHYNKHGDSKIGMAFDVMGYEPYQDSFLDDQARERSIDYNMGWFLEPVVRGDYPFSMRSLIGDRLPMFTKEEQEKLASSCDIMGLNYYTSRFSKHVDISSDYTPTLNTDDAYASSETTGSDGNEIGPITGTYWIYMYPKGLTDLLLIMKEKYGNPPIFITENGIADVEGDPEMPDPLDDWKRLDYLQRHISAVKDAIDQGADVRGHFTWGLIDNFEWGSGYSSRFGLVYIDKEDGNKRKLKKSAKWFAKFNSV 499
                                    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

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: Family 1 of glycosyl hydrolase (102)

Protein domain: automated matches (36)

Secale cereale [TaxId: 4550] (3)

d3aiva_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (HGGL_SECCE | Q9FYS3)

molecular function
	GO:0008422	beta-glucosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
	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: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: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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric Unit
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		Ala A:206 - Pro A:207	[ RasMol ]

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	3aiv
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	3.2.1.21
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	HGGL_SECCE \| Q9FYS3	:	3aiu 3aiw

2dga	HIGHLY HOMOLOGOUS PROTEIN IN WHEAT
3aiq
3air
3ais
3aiu
3aiw

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (1, 1)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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