1E56 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE INACTIVE MUTANT MONOCOT (MAIZE ZMGLU1) BETA-GLUCOSIDASE ZMGLUE191D IN COMPLEX WITH THE NATURAL SUBSTRATE DIMBOA-BETA-D-GLUCOSIDE

Authors :   M. Czjzek, M. Cicek, D. R. Bevan, V. Zamboni, B. Henrissat, A. Esen

Date :   18 Jul 00 (Deposition) - 11 Dec 00 (Release) - 16 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Glycoside Hydrolase, Beta-Glucosidase, Family 1, Retention Of The Anomeric Configuration, Inactive Mutant E191D, Complex With Dimboa-Glucoside, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Czjzek, M. Cicek, V. Zamboni, D. R. Bevan, B. Henrissat, A. Esen
The Mechanism Of Substrate (Aglycone) Specificity In Beta -Glucosidases Is Revealed By Crystal Structures Of Mutant Maize Beta -Glucosidase- Dimboa, -Dimboaglc, And -Dhurrin Complexes
Proc. Natl. Acad. Sci. Usa V. 97 13555 2000
PubMed-ID: 11106394 | Reference-DOI: 10.1073/PNAS.97.25.13555
(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 Gene	:	GLU1
	Expression System Plasmid	:	PET-21A
	Expression System Taxid	:	562
	Expression System Variant	:	PLYS S CELLS
	Mutation	:	YES
	Organelle	:	CHLOROPLAST
	Organism Common	:	MAIZE
	Organism Scientific	:	ZEA MAYS
	Organism Taxid	:	4577
	Strain	:	CV. MUTIN
	Tissue	:	COLEOPTILE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

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

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:38 , HIS A:142 , ASN A:190 , ASP A:191 , TYR A:333 , TRP A:378 , GLU A:406 , TRP A:457 , GLU A:464 , PHE A:466 , ALA A:467 , HOH A:2163 , HOH A:2167	BINDING SITE FOR POLY-SACCHARIDE RESIDUES BGC A 513 THROUGH HBO A 514
2	AC2	SOFTWARE	GLN B:38 , HIS B:142 , ASN B:190 , ASP B:191 , THR B:194 , PHE B:198 , ASP B:261 , TYR B:333 , GLU B:406 , TRP B:457 , GLU B:464 , TRP B:465 , PHE B:466 , TYR B:473 , HOH B:2148	BINDING SITE FOR POLY-SACCHARIDE RESIDUES BGC B 513 THROUGH HBO B 514

Asymmetric/Biological Unit

No.	Residues
1	A:210	-	A:216
2	B:210	-	B:216

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 1E56)

Asymmetric/Biological Unit (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.	HGGL1_MAIZE	82-96	2	A:28-42 B:28-42
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	HGGL1_MAIZE	456-464	2	A:402-410 B:402-410

(no "Exon" information available for 1E56)

Asymmetric/Biological 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:490
 aligned with HGGL1_MAIZE | P49235 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:490
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556
          HGGL1_MAIZE    67 LSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNEPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 556
               SCOP domains d1e56a_ A: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1e56A00 A:13-502 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh...eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..........hhhhhh..........................hhhhhhhhhhhhhh.....eeeee....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eeee.....eeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e56 A  13 LSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNDPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 502
                                    22        32        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

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with HGGL1_MAIZE | P49235 from UniProtKB/Swiss-Prot  Length:566

    Alignment length:490
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556
          HGGL1_MAIZE    67 LSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNEPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 556
               SCOP domains d1e56b_ B: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1e56B00 B:13-502 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..............hhhhhhhhhhhhh..eeeee.hhhhhh.........hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..........hhhhhh.........................hhhhhhhhhhhhhhh.....eeeee....ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh..ee...eeee.....eeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------GLYCOSYL_HYDROL-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e56 B  13 LSPSEIPQRDWFPSDFTFGAATSAYQIEGAWNEDGKGESNWDHFCHNHPERILDGSNSDIGANSYHMYKTDVRLLKEMGMDAYRFSISWPRILPKGTKEGGINPDGIKYYRNLINLLLENGIEPYVTIFHWDVPQALEEKYGGFLDKSHKSIVEDYTYFAKVCFDNFGDKVKNWLTFNDPQTFTSFSYGTGVFAPGRCSPGLDCAYPTGNSLVEPYTAGHNILLAHAEAVDLYNKHYKRDDTRIGLAFDVMGRVPYGTSFLDKQAEERSWDINLGWFLEPVVRGDYPFSMRSLARERLPFFKDEQKEKLAGSYNMLGLNYYTSRFSKNIDISPNYSPVLNTDDAYASQEVNGPDGKPIGPPMGNPWIYMYPEGLKDLLMIMKNKYGNPPIYITENGIGDVDTKETPLPMEAALNDYKRLDYIQRHIATLKESIDLGSNVQGYFAWSLLDNFEWFAGFTERYGIVYVDRNNNCTRYMKESAKWLKEFNTAK 502
                                    22        32        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

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/Biological 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: Plant beta-glucosidase (myrosinase) (30)

Maize (Zea mays), zmglu1 [TaxId: 4577] (9)

1a	d1e56a_	A:
1b	d1e56b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Maize. Strain: cv. Mutin. (5)

1a	1e56A00	A:13-502
1b	1e56B00	B:13-502

(no "Pfam Domain" information available for 1E56)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HGGL1_MAIZE | P49235)

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:0009736	cytokinin-activated signaling pathway	A series of molecular signals generated by the binding of a cytokinin to a receptor, and ending with regulation of a downstream cellular process, e.g. transcription.
	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/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		HBO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:206 - Pro A:207	[ RasMol ]
		Ala B:206 - Pro B:207	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1e56
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HGGL1_MAIZE \| P49235
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.21
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HGGL1_MAIZE \| P49235
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	HGGL1_MAIZE \| P49235	:	1e1e 1e1f 1e4l 1e4n 1e55 1h49 1hxj 1v08

(no "Related Entries Specified in the PDB File" available for 1E56)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (2, 2)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File