2E40 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF INTRACELLULAR FAMILY 1 BETA-GLUCOSIDASE BGL1A FROM THE BASIDIOMYCETE PHANEROCHAETE CHRYSOSPORIUM IN COMPLEX WITH GLUCONOLACTONE

Authors :   Y. Nijikken, T. Tsukada, K. Igarashi, M. Samejima, S. Fushinobu

Date :   01 Dec 06 (Deposition) - 27 Mar 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Tim Barrel, Glycoside Hydrolase Family 1, Clan Gh-A, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Nijikken, T. Tsukada, K. Igarashi, M. Samejima, T. Wakagi, H. Shoun, S. Fushinobu
Crystal Structure Of Intracellular Family 1 Beta-Glucosidase Bgl1A From The Basidiomycete Phanerochaete Chrysosporium
Febs Lett. V. 581 1514 2007
PubMed-ID: 17376440 | Reference-DOI: 10.1016/J.FEBSLET.2007.03.009
(for further references see the PDB file header)

Molecule 1 - BETA-GLUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD/TOPO THIOFUSION
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BGL1A
	Organism Scientific	:	PHANEROCHAETE CHRYSOSPORIUM
	Organism Taxid	:	5306
	Strain	:	K-3

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	LGC	2	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:20 , HIS A:123 , ASN A:169 , GLU A:170 , ASN A:299 , TYR A:301 , GLU A:365 , TRP A:415 , GLU A:422 , TRP A:423 , PHE A:431	BINDING SITE FOR RESIDUE LGC A 1001
2	AC2	SOFTWARE	GLN B:20 , HIS B:123 , ASN B:169 , GLU B:170 , ASN B:299 , TYR B:301 , GLU B:365 , TRP B:415 , GLU B:422 , TRP B:423 , PHE B:431	BINDING SITE FOR RESIDUE LGC B 2001

(no "SS Bond" information available for 2E40)

Asymmetric Unit

No.	Residues
1	Ala A:185	-	Pro A:186
2	Trp A:415	-	Ser A:416
3	Ala B:185	-	Pro B:186
4	Trp B:415	-	Ser B:416

(no "SAP(SNP)/Variant" information available for 2E40)

Asymmetric Unit (1, 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.	BGL1A_PHACH	10-24	2	A:10-24 B:10-24

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGL1A_PHACH	10-24	1	A:10-24 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGL1A_PHACH	10-24	1	- B:10-24

(no "Exon" information available for 2E40)

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:459
 aligned with BGL1A_PHACH | Q25BW5 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:459
                                    13        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         
          BGL1A_PHACH     4 AKLPKSFVWGYATAAYQIEGSPDKDGREPSIWDTFCKAPGKIADGSSGDVATDSYNRWREDVQLLKSYGVKAYRFSLSWSRIIPKGGRSDPVNGAGIKHYRTLIEELVKEGITPFVTLYHWDLPQALDDRYGGWLNKEEAIQDFTNYAKLCFESFGDLVQNWITFNEPWVISVMGYGNGIFAPGHVSNTEPWIVSHHIILAHAHAVKLYRDEFKEKQGGQIGITLDSHWLIPYDDTDASKEATLRAMEFKLGRFANPIYKGEYPPRIKKILGDRLPEFTPEEIELVKGSSDFFGLNTYTTHLVQDGGSDELAGFVKTGHTRADGTQLGTQSDMGWLQTYGPGFRWLLNYLWKAYDKPVYVTENGFPVKGENDLPVEQAVDDTDRQAYYRDYTEALLQAVTEDGADVRGYFGWSLLDNFEWAEGYKVRFGVTHVDYETQKRTPKKSAEFLSRWFKEHIEE 462
               SCOP domains d2e40a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2e40A00 A:4-462 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhh...hhhhh..hhhhhhh....................hhhhhhhhhhhh...eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeeee...hhhhh.eeee....................hhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhh....eee......eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------GLYCOSYL_HYDROL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e40 A   4 AKLPKSFVWGYATAAYQIEGSPDKDGREPSIWDTFCKAPGKIADGSSGDVATDSYNRWREDVQLLKSYGVKAYRFSLSWSRIIPKGGRSDPVNGAGIKHYRTLIEELVKEGITPFVTLYHWDLPQALDDRYGGWLNKEEAIQDFTNYAKLCFESFGDLVQNWITFNEPWVISVMGYGNGIFAPGHVSNTEPWIVSHHIILAHAHAVKLYRDEFKEKQGGQIGITLDSHWLIPYDDTDASKEATLRAMEFKLGRFANPIYKGEYPPRIKKILGDRLPEFTPEEIELVKGSSDFFGLNTYTTHLVQDGGSDELAGFVKTGHTRADGTQLGTQSDMGWLQTYGPGFRWLLNYLWKAYDKPVYVTENGFPVKGENDLPVEQAVDDTDRQAYYRDYTEALLQAVTEDGADVRGYFGWSLLDNFEWAEGYKVRFGVTHVDYETQKRTPKKSAEFLSRWFKEHIEE 462
                                    13        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

Chain B from PDB  Type:PROTEIN  Length:459
 aligned with BGL1A_PHACH | Q25BW5 from UniProtKB/Swiss-Prot  Length:462

    Alignment length:459
                                    13        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         
          BGL1A_PHACH     4 AKLPKSFVWGYATAAYQIEGSPDKDGREPSIWDTFCKAPGKIADGSSGDVATDSYNRWREDVQLLKSYGVKAYRFSLSWSRIIPKGGRSDPVNGAGIKHYRTLIEELVKEGITPFVTLYHWDLPQALDDRYGGWLNKEEAIQDFTNYAKLCFESFGDLVQNWITFNEPWVISVMGYGNGIFAPGHVSNTEPWIVSHHIILAHAHAVKLYRDEFKEKQGGQIGITLDSHWLIPYDDTDASKEATLRAMEFKLGRFANPIYKGEYPPRIKKILGDRLPEFTPEEIELVKGSSDFFGLNTYTTHLVQDGGSDELAGFVKTGHTRADGTQLGTQSDMGWLQTYGPGFRWLLNYLWKAYDKPVYVTENGFPVKGENDLPVEQAVDDTDRQAYYRDYTEALLQAVTEDGADVRGYFGWSLLDNFEWAEGYKVRFGVTHVDYETQKRTPKKSAEFLSRWFKEHIEE 462
               SCOP domains d2e40b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2e40B00 B:4-462 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhh..........hhhhhhh....................hhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhh.....eeee...eeeeee...hhhhh.eeee....................hhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeeeee......hhhhh.......eee......eeehhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------GLYCOSYL_HYDROL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e40 B   4 AKLPKSFVWGYATAAYQIEGSPDKDGREPSIWDTFCKAPGKIADGSSGDVATDSYNRWREDVQLLKSYGVKAYRFSLSWSRIIPKGGRSDPVNGAGIKHYRTLIEELVKEGITPFVTLYHWDLPQALDDRYGGWLNKEEAIQDFTNYAKLCFESFGDLVQNWITFNEPWVISVMGYGNGIFAPGHVSNTEPWIVSHHIILAHAHAVKLYRDEFKEKQGGQIGITLDSHWLIPYDDTDASKEATLRAMEFKLGRFANPIYKGEYPPRIKKILGDRLPEFTPEEIELVKGSSDFFGLNTYTTHLVQDGGSDELAGFVKTGHTRADGTQLGTQSDMGWLQTYGPGFRWLLNYLWKAYDKPVYVTENGFPVKGENDLPVEQAVDDTDRQAYYRDYTEALLQAVTEDGADVRGYFGWSLLDNFEWAEGYKVRFGVTHVDYETQKRTPKKSAEFLSRWFKEHIEE 462
                                    13        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

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)

Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306] (2)

1a	d2e40a_	A:
1b	d2e40b_	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)

Phanerochaete chrysosporium. Organism_taxid: 5306. Strain: k-3. (2)

1a	2e40A00	A:4-462
1b	2e40B00	B:4-462

(no "Pfam Domain" information available for 2E40)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BGL1A_PHACH | Q25BW5)

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:0080079	cellobiose glucosidase activity	Catalysis of the reaction: cellobiose + H2O = 2 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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:185 - Pro A:186	[ RasMol ]
		Ala B:185 - Pro B:186	[ RasMol ]
		Trp A:415 - Ser A:416	[ RasMol ]
		Trp B:415 - Ser B:416	[ RasMol ]

Biological Units
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	2e40
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	BGL1A_PHACH \| Q25BW5	:	2e3z

2e3z	THE SAME STRUCTURE WITHOUT SUBSTRATE

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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