1E6X - JenaLib

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Title :   MYROSINASE FROM SINAPIS ALBA WITH A BOUND TRANSITION STATE ANALOGUE,D-GLUCONO-1,5-LACTONE

Authors :   W. P. Burmeister

Date :   23 Aug 00 (Deposition) - 05 Jan 01 (Release) - 19 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Family 1 Glycosyl Hydrolase, Glucosinolate, Tim Barrel, Hydrolase (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	:	3.2.3.1
	Organ	:	SEED
	Organism Common	:	WHITE MUSTARD
	Organism Scientific	:	SINAPIS ALBA
	Organism Taxid	:	3728
	Strain	:	EMERGO
	Synonym	:	THIOGLUCOSIDE GLUCOHYDROLASE, SINIGRINASE, THIOGLUCOSIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (9, 33)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GOL	4	Ligand/Ion	GLYCEROL
4	LGC	1	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
5	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	8	Ligand/Ion	SULFATE ION
8	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
9	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (8, 64)

No.	Name	Count	Type	Full Name
1	BMA	4	Ligand/Ion	BETA-D-MANNOSE
2	FUC	4	Ligand/Ion	ALPHA-L-FUCOSE
3	GOL	8	Ligand/Ion	GLYCEROL
4	LGC	2	Ligand/Ion	(3S,4R,5R,6S)-3,4,5-TRIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-ONE
5	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	24	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	16	Ligand/Ion	SULFATE ION
8	XYP	4	Ligand/Ion	BETA-D-XYLOPYRANOSE
9	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (23, 23)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , ASN M:328 , TYR M:330 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , PHE M:473 , HOH M:2763 , HOH M:2764 , HOH M:2765	BINDING SITE FOR RESIDUE LGC M 999
02	AC2	SOFTWARE	HIS M:56 , ASP M:70	BINDING SITE FOR RESIDUE ZN M1502
03	AC3	SOFTWARE	ARG M:205 , HOH M:2375 , HOH M:2767 , HOH M:2768 , HOH M:2769 , HOH M:2770	BINDING SITE FOR RESIDUE SO4 M1503
04	AC4	SOFTWARE	LYS M:108 , ARG M:111 , HOH M:2225 , HOH M:2303 , HOH M:2771 , HOH M:2772	BINDING SITE FOR RESIDUE SO4 M1504
05	AC5	SOFTWARE	ARG M:259 , GLN M:333 , SO4 M:1510 , HOH M:2773 , HOH M:2775 , HOH M:2792	BINDING SITE FOR RESIDUE SO4 M1505
06	AC6	SOFTWARE	GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2009 , HOH M:2776 , HOH M:2777 , HOH M:2778 , HOH M:2779 , HOH M:2780	BINDING SITE FOR RESIDUE SO4 M1506
07	AC7	SOFTWARE	HIS M:270 , ALA M:273 , ARG M:277 , HOH M:2782 , HOH M:2783 , HOH M:2784 , HOH M:2785	BINDING SITE FOR RESIDUE SO4 M1507
08	AC8	SOFTWARE	ARG M:109 , VAL M:113 , GLU M:173 , HOH M:2786 , HOH M:2787 , HOH M:2788	BINDING SITE FOR RESIDUE SO4 M1508
09	AC9	SOFTWARE	ASN M:60 , HIS M:66 , NAG M:961	BINDING SITE FOR RESIDUE SO4 M1509
10	BC1	SOFTWARE	ARG M:194 , ARG M:259 , SO4 M:1505 , HOH M:2352 , HOH M:2773 , HOH M:2791 , HOH M:2792 , HOH M:2793 , HOH M:2794	BINDING SITE FOR RESIDUE SO4 M1510
11	BC2	SOFTWARE	ASN M:316 , LEU M:317 , HOH M:2385 , HOH M:2389 , HOH M:2486 , HOH M:2795 , HOH M:2796 , HOH M:2797 , HOH M:2798	BINDING SITE FOR RESIDUE GOL M1511
12	BC3	SOFTWARE	ILE M:50 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2301 , HOH M:2307 , HOH M:2799	BINDING SITE FOR RESIDUE GOL M1512
13	BC4	SOFTWARE	HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2409 , HOH M:2453 , HOH M:2800 , HOH M:2801 , HOH M:2802	BINDING SITE FOR RESIDUE GOL M1513
14	BC5	SOFTWARE	GLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2276 , HOH M:2803 , HOH M:2804	BINDING SITE FOR RESIDUE GOL M1514
15	BC6	SOFTWARE	THR M:17 , ASP M:18 , ASN M:21 , SER M:24 , HOH M:2712 , HOH M:2713 , HOH M:2714	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 21 RESIDUES 901 TO 901
16	BC7	SOFTWARE	TYR M:58 , ASN M:60 , SER M:213 , SO4 M:1509 , HOH M:2119 , HOH M:2371 , HOH M:2759 , HOH M:2760	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 60 RESIDUES 961 TO 961
17	BC8	SOFTWARE	ASN M:90 , SER M:500 , HOH M:2715 , HOH M:2718 , HOH M:2719	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 90 RESIDUES 911 TO 911
18	BC9	SOFTWARE	SER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:2720 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724 , HOH M:2726	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
19	CC1	SOFTWARE	LYS M:165 , LEU M:240 , ASN M:244 , HOH M:2390 , HOH M:2399	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 244 RESIDUES 931 TO 931
20	CC2	SOFTWARE	ASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , SER M:363 , HOH M:2433 , HOH M:2487 , HOH M:2729 , HOH M:2731 , HOH M:2733 , HOH M:2734 , HOH M:2735 , HOH M:2736 , HOH M:2738 , HOH M:2739	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
21	CC3	SOFTWARE	ILE M:129 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:1514 , HOH M:2269 , HOH M:2344 , HOH M:2452 , HOH M:2453 , HOH M:2455 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2744 , HOH M:2745 , HOH M:2747 , HOH M:2749 , HOH M:2750 , HOH M:2752 , HOH M:2753 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2800	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 956
22	CC4	SOFTWARE	ASN M:346 , HOH M:2528	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 346 RESIDUES 971 TO 971
23	CC5	SOFTWARE	ASN M:482 , ASP M:485 , HOH M:2692 , HOH M:2761	BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 482 RESIDUES 991 TO 991

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 1E6X)

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 1E6X)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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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 d1e6xm_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e6xM00 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
                 1e6x 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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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

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)

d1e6xm_

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)

1e6xM00

M:3-501

(no "Pfam Domain" information available for 1E6X)

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.

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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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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
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
1e73	2-F-GLUCOSYLATED MYROSINASE FROM SINAPIS ALBA WITH BOUND L-ASCORBATE
1myr	MYROSINASE FROM SINAPIS ALBA
2myr	MYROSINASE, 2-DEOXY-2-FLUORO-GLUCOSYL ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 33)

Sites (23, 23)

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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