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(-) Description

Title :  S. ALBA MYROSINASE IN COMPLEX WITH CARBA-GLUCOTROPAEOLIN
 
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 :  1.70
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

Molecule 1 - GLYCOSIDASE
    Chains: M
    EC Number: 3.2.3.1
    Organ: SEED
    Organism Common: WHITE MUSTARD
    Organism Scientific: SINAPIS ALBA
    Organism Taxid: 3728
    Strain: EMERGO
    Synonym: MYROSINASE
    Tissue: MYROSIN GRAINS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 31)

Asymmetric/Biological Unit (9, 31)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CGT1Ligand/IonCARBA-GLUCOTROPAEOLIN
3FUC2Ligand/IonALPHA-L-FUCOSE
4GOL3Ligand/IonGLYCEROL
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO44Ligand/IonSULFATE ION
8XYP2Ligand/IonBETA-D-XYLOPYRANOSE
9ZN1Ligand/IonZINC ION

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , HOH M:2049 , HOH M:2672 , HOH M:2673BINDING SITE FOR RESIDUE NAG M 901
02AC2SOFTWAREASN M:90 , SER M:500 , MAN M:957 , HOH M:2669 , HOH M:2674 , HOH M:2675BINDING SITE FOR RESIDUE NAG M 911
03AC3SOFTWAREASN M:218 , THR M:221 , NAG M:923 , HOH M:2676 , HOH M:2677 , HOH M:2678 , HOH M:2679 , HOH M:2680BINDING SITE FOR RESIDUE NAG M 921
04AC4SOFTWAREGLU M:305 , NAG M:921 , HOH M:2681BINDING SITE FOR RESIDUE NAG M 923
05AC5SOFTWARELYS M:165 , LEU M:240 , ASN M:244 , HOH M:2684BINDING SITE FOR RESIDUE NAG M 931
06AC6SOFTWAREASN M:265 , ASP M:268 , ALA M:362 , FUC M:942 , NAG M:943 , HOH M:2685 , HOH M:2686 , HOH M:2687 , HOH M:2689BINDING SITE FOR RESIDUE NAG M 941
07AC7SOFTWARENAG M:941 , NAG M:943BINDING SITE FOR RESIDUE FUC M 942
08AC8SOFTWAREASN M:316 , NAG M:941 , FUC M:942 , BMA M:944 , XYP M:945 , HOH M:2689 , HOH M:2691 , HOH M:2692 , HOH M:2694BINDING SITE FOR RESIDUE NAG M 943
09AC9SOFTWARENAG M:943 , XYP M:945BINDING SITE FOR RESIDUE BMA M 944
10BC1SOFTWAREASN M:316 , LYS M:319 , NAG M:943 , BMA M:944 , HOH M:2692 , HOH M:2695BINDING SITE FOR RESIDUE XYP M 945
11BC2SOFTWAREASN M:292 , THR M:294 , FUC M:952 , NAG M:953 , HOH M:2426 , HOH M:2430 , HOH M:2696 , HOH M:2697 , HOH M:2762BINDING SITE FOR RESIDUE NAG M 951
12BC3SOFTWAREILE M:129 , GLN M:297 , NAG M:951 , NAG M:953 , HOH M:2700 , HOH M:2701 , HOH M:2702 , HOH M:2704 , HOH M:2762BINDING SITE FOR RESIDUE FUC M 952
13BC4SOFTWAREGLN M:297 , NAG M:951 , FUC M:952 , BMA M:954 , XYP M:955 , MAN M:956 , HOH M:2260 , HOH M:2705 , HOH M:2706 , HOH M:2713 , HOH M:2717BINDING SITE FOR RESIDUE NAG M 953
14BC5SOFTWARENAG M:953 , XYP M:955 , MAN M:956 , MAN M:957 , HOH M:2708 , HOH M:2711 , HOH M:2713BINDING SITE FOR RESIDUE BMA M 954
15BC6SOFTWARENAG M:953 , BMA M:954 , MAN M:956 , HOH M:2713 , HOH M:2714BINDING SITE FOR RESIDUE XYP M 955
16BC7SOFTWAREGLN M:297 , ILE M:300 , NAG M:953 , BMA M:954 , XYP M:955 , HOH M:2716 , HOH M:2717 , HOH M:2718 , HOH M:2719BINDING SITE FOR RESIDUE MAN M 956
17BC8SOFTWARETHR M:92 , NAG M:911 , BMA M:954 , HOH M:2711 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724BINDING SITE FOR RESIDUE MAN M 957
18BC9SOFTWAREASN M:60 , HOH M:2111 , HOH M:2119 , HOH M:2728 , HOH M:2729BINDING SITE FOR RESIDUE NAG M 961
19CC1SOFTWAREASN M:346 , MET M:351 , HOH M:2498BINDING SITE FOR RESIDUE NAG M 971
20CC2SOFTWAREASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , NAG M:983 , HOH M:2395 , HOH M:2399 , HOH M:2478BINDING SITE FOR RESIDUE NAG M 981
21CC3SOFTWAREPRO M:11 , NAG M:981 , HOH M:2005 , HOH M:2735 , HOH M:2736BINDING SITE FOR RESIDUE NAG M 983
22CC4SOFTWAREASN M:482 , ASP M:485 , HOH M:2737 , HOH M:2738BINDING SITE FOR RESIDUE NAG M 991
23CC5SOFTWAREHIS M:56 , ASP M:70BINDING SITE FOR RESIDUE ZN M1502
24CC6SOFTWAREGLU M:153 , ARG M:205 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2747BINDING SITE FOR RESIDUE SO4 M1503
25CC7SOFTWARELYS M:108 , ARG M:111 , HOH M:2222 , HOH M:2749 , HOH M:2750 , HOH M:2751BINDING SITE FOR RESIDUE SO4 M1504
26CC8SOFTWAREARG M:259 , GLN M:333 , LEU M:357 , HOH M:2333 , HOH M:2752BINDING SITE FOR RESIDUE SO4 M1505
27CC9SOFTWAREGLN M:7 , GLU M:8 , ASN M:9 , HOH M:2754 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2759BINDING SITE FOR RESIDUE SO4 M1506
28DC1SOFTWAREGLN M:187 , TYR M:189 , SER M:190 , ARG M:194 , ILE M:257 , ARG M:259 , TYR M:330 , PHE M:371 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , PHE M:473 , GOL M:1000 , HOH M:2532 , HOH M:2636 , HOH M:2739 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2743BINDING SITE FOR RESIDUE CGT M 999
29DC2SOFTWAREGLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , CGT M:999 , HOH M:2742 , HOH M:2743BINDING SITE FOR RESIDUE GOL M1000
30DC3SOFTWAREPHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2296 , HOH M:2760BINDING SITE FOR RESIDUE GOL M1512
31DC4SOFTWARETHR M:246 , HIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2701 , HOH M:2761 , HOH M:2762 , HOH M:2763 , HOH M:2764BINDING SITE FOR RESIDUE GOL M1513

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1M:6 -M:438
2M:14 -M:434
3M:206 -M:214

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu M:10 -Pro M:11
2Ala M:202 -Pro M:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W9B)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.MYRA_SINAL29-43  1M:29-43
2GLYCOSYL_HYDROL_F1_1PS00572 Glycosyl hydrolases family 1 active site.MYRA_SINAL405-413  1M:405-413

(-) Exons   (0, 0)

(no "Exon" information available for 1W9B)

(-) 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 d1w9bm_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w9bM00 M:3-501 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------Glyco_hydro_1-1w9bM01 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
                 1w9b 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)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) 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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  MYRA_SINAL | P29736
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MYRA_SINAL | P29736: 1dwa 1dwf 1dwg 1dwh 1dwi 1dwj 1e4m 1e6q 1e6s 1e6x 1e70 1e71 1e72 1e73 1myr 1w9d 2wxd

(-) Related Entries Specified in the PDB File

1myr MYROSINASE FROM SINAPIS ALBA
1w9d S. ALBA MYROSINASE IN COMPLEX WITH S-ETHYL PHENYLACETOTHIOHYDROXIMATE-O-SULFATE