1W9D - JenaLib

Title :   S. ALBA MYROSINASE IN COMPLEX WITH S-ETHYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE

Authors :   A. Bourderioux, M. Lefoix, D. Gueyrard, A. Tatibouet, S. Cottaz, S. Arzt, W. P. Burmeister, P. Rollin

Date :   08 Oct 04 (Deposition) - 19 May 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : M

Keywords :   Thioglucosidase, Thioglycosidase, Myrosinase, Hydrolase, Thio-Glucoside, Thiohydroximate, Glusosinolate, Glucotropaeolin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Bourderioux, M. Lefoix, D. Gueyrard, A. Tatibouet, S. Cottaz, S. Arzt, W. P. Burmeister, P. Rollin
The Glucosinolate-Myrosinase System. New Insights Into Enzyme-Substrate Interactions By Use Of Simplified Inhibitors
Org. Biomol. Chem. V. 3 1872 2005
PubMed-ID: 15889170 | Reference-DOI: 10.1039/B502990B
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 31)

Sites (31, 31)

Asymmetric Unit (31, 31)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:2049 , HOH M:2674 , HOH M:2675	BINDING SITE FOR RESIDUE NAG M 901
02	AC2	SOFTWARE	ASN M:90 , SER M:500 , MAN M:957 , HOH M:2676 , HOH M:2677 , HOH M:2679	BINDING SITE FOR RESIDUE NAG M 911
03	AC3	SOFTWARE	ASN M:218 , THR M:221 , NAG M:923 , HOH M:2680 , HOH M:2681 , HOH M:2682 , HOH M:2683 , HOH M:2684	BINDING SITE FOR RESIDUE NAG M 921
04	AC4	SOFTWARE	GLU M:305 , NAG M:921 , HOH M:2685	BINDING SITE FOR RESIDUE NAG M 923
05	AC5	SOFTWARE	LYS M:165 , LEU M:240 , ASN M:244 , HOH M:2688	BINDING SITE FOR RESIDUE NAG M 931
06	AC6	SOFTWARE	ASN M:265 , ASP M:268 , ALA M:362 , FUC M:942 , NAG M:943 , HOH M:2689 , HOH M:2690 , HOH M:2691 , HOH M:2692 , HOH M:2697	BINDING SITE FOR RESIDUE NAG M 941
07	AC7	SOFTWARE	NAG M:941 , NAG M:943	BINDING SITE FOR RESIDUE FUC M 942
08	AC8	SOFTWARE	ASN M:316 , NAG M:941 , FUC M:942 , BMA M:944 , XYP M:945 , HOH M:2694 , HOH M:2695 , HOH M:2697 , HOH M:2698	BINDING SITE FOR RESIDUE NAG M 943
09	AC9	SOFTWARE	NAG M:943 , XYP M:945	BINDING SITE FOR RESIDUE BMA M 944
10	BC1	SOFTWARE	ASN M:316 , LYS M:319 , NAG M:943 , BMA M:944 , HOH M:2695 , HOH M:2699	BINDING SITE FOR RESIDUE XYP M 945
11	BC2	SOFTWARE	ASN M:292 , THR M:294 , FUC M:952 , NAG M:953 , HOH M:2431 , HOH M:2434 , HOH M:2700 , HOH M:2701	BINDING SITE FOR RESIDUE NAG M 951
12	BC3	SOFTWARE	ILE M:129 , GLN M:297 , NAG M:951 , NAG M:953 , HOH M:2326 , HOH M:2704 , HOH M:2705 , HOH M:2706 , HOH M:2760	BINDING SITE FOR RESIDUE FUC M 952
13	BC4	SOFTWARE	GLN M:297 , NAG M:951 , FUC M:952 , BMA M:954 , XYP M:955 , MAN M:956 , HOH M:2262 , HOH M:2708 , HOH M:2709 , HOH M:2716 , HOH M:2719	BINDING SITE FOR RESIDUE NAG M 953
14	BC5	SOFTWARE	NAG M:953 , XYP M:955 , MAN M:956 , MAN M:957 , HOH M:2711 , HOH M:2712 , HOH M:2714 , HOH M:2716	BINDING SITE FOR RESIDUE BMA M 954
15	BC6	SOFTWARE	NAG M:953 , BMA M:954 , MAN M:956 , HOH M:2716 , HOH M:2717	BINDING SITE FOR RESIDUE XYP M 955
16	BC7	SOFTWARE	GLN M:297 , ILE M:300 , NAG M:953 , BMA M:954 , XYP M:955 , HOH M:2718 , HOH M:2719 , HOH M:2720 , HOH M:2721	BINDING SITE FOR RESIDUE MAN M 956
17	BC8	SOFTWARE	THR M:92 , NAG M:911 , BMA M:954 , HOH M:2714 , HOH M:2724 , HOH M:2725 , HOH M:2726 , HOH M:2727	BINDING SITE FOR RESIDUE MAN M 957
18	BC9	SOFTWARE	ASN M:60 , HOH M:2111 , HOH M:2121 , HOH M:2730	BINDING SITE FOR RESIDUE NAG M 961
19	CC1	SOFTWARE	ASN M:346 , MET M:351 , HOH M:2504	BINDING SITE FOR RESIDUE NAG M 971
20	CC2	SOFTWARE	ASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , NAG M:983 , HOH M:2399 , HOH M:2404 , HOH M:2483 , HOH M:2734	BINDING SITE FOR RESIDUE NAG M 981
21	CC3	SOFTWARE	PRO M:11 , NAG M:981 , HOH M:2736 , HOH M:2737	BINDING SITE FOR RESIDUE NAG M 983
22	CC4	SOFTWARE	ASN M:482 , ASP M:485 , HOH M:2738 , HOH M:2739	BINDING SITE FOR RESIDUE NAG M 991
23	CC5	SOFTWARE	HIS M:56 , ASP M:70	BINDING SITE FOR RESIDUE ZN M1502
24	CC6	SOFTWARE	GLU M:153 , ARG M:205 , HOH M:2358 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2743	BINDING SITE FOR RESIDUE SO4 M1503
25	CC7	SOFTWARE	LYS M:108 , ARG M:111 , HOH M:2745 , HOH M:2746 , HOH M:2747 , HOH M:2748	BINDING SITE FOR RESIDUE SO4 M1504
26	CC8	SOFTWARE	ARG M:259 , GLN M:333 , LEU M:357 , HOH M:2336 , HOH M:2749	BINDING SITE FOR RESIDUE SO4 M1505
27	CC9	SOFTWARE	GLN M:7 , GLU M:8 , ASN M:9 , HOH M:2751 , HOH M:2752 , HOH M:2753 , HOH M:2754 , HOH M:2755 , HOH M:2756	BINDING SITE FOR RESIDUE SO4 M1506
28	DC1	SOFTWARE	GLN M:187 , TYR M:189 , SER M:190 , ARG M:194 , ILE M:257 , ARG M:259 , PHE M:282 , TYR M:330 , PHE M:371 , GOL M:1514 , HOH M:2148 , HOH M:2338	BINDING SITE FOR RESIDUE SEH M 999
29	DC2	SOFTWARE	PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2290 , HOH M:2757 , HOH M:2758	BINDING SITE FOR RESIDUE GOL M1512
30	DC3	SOFTWARE	HIS M:247 , GLN M:248 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2386 , HOH M:2705 , HOH M:2759 , HOH M:2760 , HOH M:2761	BINDING SITE FOR RESIDUE GOL M1513
31	DC4	SOFTWARE	GLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , SEH M:999	BINDING SITE FOR RESIDUE GOL M1514

SS Bonds (3, 3)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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 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 d1w9dm_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w9dM00 M:3-501 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------Glyco_hydro_1-1w9dM01 M:21-501                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author ..................hhhhh....eeeee.hhhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeeeeeeeeeee..........hhhhhh.eeee...........eee....hhhhhee..hhhhhhhhhhhhhhh....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.............ee...eeee..eeeeeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w9d 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

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological 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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	1w9d
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