1E73 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   2-F-GLUCOSYLATED MYROSINASE FROM SINAPIS ALBA WITH BOUND L-ASCORBATE

Authors :   W. P. Burmeister

Date :   23 Aug 00 (Deposition) - 05 Jan 01 (Release) - 14 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym. Unit : M
Biol. Unit 1: M  (2x)

Keywords :   Hydrolase, Family 1 Glycosyl Hydrolase, Glucosinolate, Myrosinase, Tim Barrel, Ascorbate, Activation, Glucosyl Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. P. Burmeister, S. Cottaz, P. Rollin, A. Vasella, B. Henrissat
High Resolution X-Ray Crystallography Shows That Ascorbate Is A Cofactor For Myrosinase And Substitutes For The Function Of The Catalytic Base
J. Biol. Chem. V. 275 39385 2000
PubMed-ID: 10978344 | Reference-DOI: 10.1074/JBC.M006796200
(for further references see the PDB file header)

Molecule 1 - MYROSINASE MA1
	Cellular Location	:	MYROSIN GRAINS
	Chains	:	M
	EC Number	:	3.2.1.147
	Organ	:	SEED
	Organism Common	:	WHITE MUSTARD
	Organism Scientific	:	SINAPIS ALBA
	Organism Taxid	:	3728
	Strain	:	EMERGO
	Synonym	:	THIOGLUCOSIDE GLUCOHYDROLASE

		1
Asymmetric Unit	:	M
Biological Unit 1 (2x)	:	M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (10, 35)

No.	Name	Count	Type	Full Name
1	ASC	1	Ligand/Ion	ASCORBIC ACID
2	BMA	2	Ligand/Ion	BETA-D-MANNOSE
3	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
4	G2F	1	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE
5	GOL	4	Ligand/Ion	GLYCEROL
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	SO4	8	Ligand/Ion	SULFATE ION
9	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
10	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (9, 68)

No.	Name	Count	Type	Full Name
1	ASC	2	Ligand/Ion	ASCORBIC ACID
2	BMA	4	Ligand/Ion	BETA-D-MANNOSE
3	FUC	4	Ligand/Ion	ALPHA-L-FUCOSE
4	G2F	2	Ligand/Ion	2-DEOXY-2-FLUORO-ALPHA-D-GLUCOPYRANOSE
5	GOL	8	Ligand/Ion	GLYCEROL
6	MAN	4	Ligand/Ion	ALPHA-D-MANNOSE
7	NAG	24	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	SO4	16	Ligand/Ion	SULFATE ION
9	XYP	4	Ligand/Ion	BETA-D-XYLOPYRANOSE
10	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR M:17 , ASP M:18 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:2703 , HOH M:2704 , HOH M:2705	BINDING SITE FOR RESIDUE NAG M 901
02	AC2	SOFTWARE	ASN M:90 , SER M:500 , MAN M:957 , HOH M:2706 , HOH M:2708 , HOH M:2709	BINDING SITE FOR RESIDUE NAG M 911
03	AC3	SOFTWARE	LYS M:165 , LEU M:240 , ASN M:244 , HOH M:2382	BINDING SITE FOR RESIDUE NAG M 931
04	AC4	SOFTWARE	TYR M:58 , ASN M:60 , SER M:213 , SO4 M:1508 , HOH M:2117 , HOH M:2754	BINDING SITE FOR RESIDUE NAG M 961
05	AC5	SOFTWARE	SER M:344 , ASN M:346 , HOH M:2755	BINDING SITE FOR RESIDUE NAG M 971
06	AC6	SOFTWARE	ASN M:482 , ASP M:485 , HOH M:2680 , HOH M:2684	BINDING SITE FOR RESIDUE NAG M 991
07	AC7	SOFTWARE	GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , TYR M:330 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , PHE M:473 , ASC M:995 , HOH M:2348 , HOH M:2757	BINDING SITE FOR RESIDUE G2F M 999
08	AC8	SOFTWARE	ARG M:205 , HOH M:2762 , HOH M:2763 , HOH M:2764 , HOH M:2765	BINDING SITE FOR RESIDUE SO4 M1502
09	AC9	SOFTWARE	LYS M:108 , ARG M:111 , HOH M:2204 , HOH M:2217 , HOH M:2298 , HOH M:2766	BINDING SITE FOR RESIDUE SO4 M1503
10	BC1	SOFTWARE	ARG M:259 , GLN M:333 , SO4 M:1509 , HOH M:2767 , HOH M:2768 , HOH M:2769 , HOH M:2770	BINDING SITE FOR RESIDUE SO4 M1504
11	BC2	SOFTWARE	GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2009 , HOH M:2771 , HOH M:2772 , HOH M:2773 , HOH M:2774 , HOH M:2775	BINDING SITE FOR RESIDUE SO4 M1505
12	BC3	SOFTWARE	HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2776 , HOH M:2777 , HOH M:2778 , HOH M:2779	BINDING SITE FOR RESIDUE SO4 M1506
13	BC4	SOFTWARE	ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2209 , HOH M:2780 , HOH M:2781	BINDING SITE FOR RESIDUE SO4 M1507
14	BC5	SOFTWARE	ASN M:60 , HIS M:66 , NAG M:961	BINDING SITE FOR RESIDUE SO4 M1508
15	BC6	SOFTWARE	ARG M:194 , ARG M:259 , SO4 M:1504 , HOH M:2759 , HOH M:2767 , HOH M:2768 , HOH M:2783 , HOH M:2784 , HOH M:2785	BINDING SITE FOR RESIDUE SO4 M1509
16	BC7	SOFTWARE	HIS M:56 , ASP M:70	BINDING SITE FOR RESIDUE ZN M1515
17	BC8	SOFTWARE	GLN M:187 , ILE M:257 , ARG M:259 , TYR M:330 , PHE M:331 , PHE M:473 , G2F M:999 , HOH M:2348 , HOH M:2411 , HOH M:2554 , HOH M:2556 , HOH M:2757 , HOH M:2758 , HOH M:2759 , HOH M:2760	BINDING SITE FOR RESIDUE ASC M 995
18	BC9	SOFTWARE	ARG M:269 , ASN M:316 , LEU M:317 , HOH M:2381 , HOH M:2384 , HOH M:2478 , HOH M:2786 , HOH M:2787 , HOH M:2788	BINDING SITE FOR RESIDUE GOL M1510
19	CC1	SOFTWARE	ILE M:50 , GLY M:53 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2302 , HOH M:2789	BINDING SITE FOR RESIDUE GOL M1511
20	CC2	SOFTWARE	HIS M:247 , GLN M:248 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2402 , HOH M:2790 , HOH M:2791 , HOH M:2792 , HOH M:2793	BINDING SITE FOR RESIDUE GOL M1512
21	CC3	SOFTWARE	GLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2794 , HOH M:2795	BINDING SITE FOR RESIDUE GOL M1513
22	CC4	SOFTWARE	SER M:207 , ASN M:218 , THR M:221 , HOH M:2456 , HOH M:2710 , HOH M:2711 , HOH M:2712 , HOH M:2713 , HOH M:2714	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
23	CC5	SOFTWARE	ASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , HOH M:2477 , HOH M:2716 , HOH M:2718 , HOH M:2719 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724 , HOH M:2726 , HOH M:2727	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
24	CC6	SOFTWARE	THR M:92 , ILE M:129 , GLY M:132 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , NAG M:911 , GOL M:1513 , HOH M:2343 , HOH M:2440 , HOH M:2443 , HOH M:2729 , HOH M:2730 , HOH M:2731 , HOH M:2733 , HOH M:2734 , HOH M:2737 , HOH M:2740 , HOH M:2741 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2747 , HOH M:2748 , HOH M:2749 , HOH M:2750 , HOH M:2751 , HOH M:2752 , HOH M:2791 , HOH M:2792	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957

Asymmetric Unit

No.	Residues
1	M:6	-	M:438
2	M:14	-	M:434
3	M:206	-	M:214

Asymmetric Unit

No.	Residues
1	Leu M:10	-	Pro M:11
2	Ala M:202	-	Pro M:203
3	Trp M:457	-	Ala M:458

(no "SAP(SNP)/Variant" information available for 1E73)

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.	MYRA_SINAL	29-43	1	M:29-43
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	MYRA_SINAL	405-413	1	M:405-413

Biological Unit 1 (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.	MYRA_SINAL	29-43	2	M:29-43
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	MYRA_SINAL	405-413	2	M:405-413

(no "Exon" information available for 1E73)

Asymmetric Unit

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	UniProt sequence: complete aligned part

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Chain M from PDB  Type:PROTEIN  Length:499
 aligned with MYRA_SINAL | P29736 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:499
                                    12        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         
           MYRA_SINAL     3 EITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDTVGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMDAGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQSFISP 501
               SCOP domains d1e73m_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e73M00 M:3-501 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh....eeeee.hhhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.eeee.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeee..eeeeee..........hhhhhh.eeee..................hhhhh....hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee................................hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e73 M   3 EITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDTVGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMDAGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQSFISP 501
                                    12        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

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

White mustard (Sinapis alba) [TaxId: 3728] (18)

d1e73m_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

White mustard (Sinapis alba) (18)

1e73M00

M:3-501

(no "Pfam Domain" information available for 1E73)

Asymmetric Unit(hide GO term definitions)

Chain M (MYRA_SINAL | P29736)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0019137	thioglucosidase activity	Catalysis of the reaction: a thioglucoside + H2O = a thiol + a sugar.
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:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala M:202 - Pro M:203	[ RasMol ]
		Leu M:10 - Pro M:11	[ RasMol ]
		Trp M:457 - Ala M:458	[ RasMol ]

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	1e73
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	3.2.1.147
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1e4m	MYROSINASE FROM SINAPIS ALBA
1e6q	MYROSINASE FROM SINAPIS ALBA WITH THE BOUND TRANSITION STATE ANALOGUE GLUCO-TETRAZOLE
1e6s	MYROSINASE FROM SINAPIS ALBA WITH BOUND GLUCO-HYDROXIMOLACTAM AND SULFATE
1e6x	MYROSINASE FROM SINAPIS ALBA WITH A BOUND TRANSITION STATE ANALOGUE,D-GLUCONO-1,5-LACTONE
1e70	2-F-GLUCOSYLATED MYROSINASE FROM SINAPIS ALBA
1e71	MYROSINASE FROM SINAPIS ALBA WITH BOUND ASCORBATE
1e72	MYROSINASE FROM SINAPIS ALBA WITH BOUND GLUCO-HYDROXIMOLACTAM AND SULFATE OR ASCORBATE
1myr	MYROSINASE FROM SINAPIS ALBA
2myr	MYROSINASE, 2-DEOXY-2-FLUORO-GLUCOSYL ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (10, 35)

Sites (24, 24)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

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Gene Ontology (8, 8)

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