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(-) Description

Title :  MYROSINASE FROM SINAPIS ALBA WITH BOUND ASCORBATE
 
Authors :  W. P. Burmeister
Date :  23 Aug 00  (Deposition) - 05 Jan 01  (Release) - 30 Nov 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, Tim Barrel, Activation (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)

(-) Compounds

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: THIOGLUCOSIDASE, SINIGRINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 35)

Asymmetric Unit (9, 35)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2BMA2Ligand/IonBETA-D-MANNOSE
3FUC2Ligand/IonALPHA-L-FUCOSE
4GOL5Ligand/IonGLYCEROL
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO48Ligand/IonSULFATE ION
8XYP2Ligand/IonBETA-D-XYLOPYRANOSE
9ZN1Ligand/IonZINC ION
Biological Unit 1 (8, 68)
No.NameCountTypeFull Name
1ASC2Ligand/IonASCORBIC ACID
2BMA4Ligand/IonBETA-D-MANNOSE
3FUC4Ligand/IonALPHA-L-FUCOSE
4GOL10Ligand/IonGLYCEROL
5MAN4Ligand/IonALPHA-D-MANNOSE
6NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO416Ligand/IonSULFATE ION
8XYP4Ligand/IonBETA-D-XYLOPYRANOSE
9ZN-1Ligand/IonZINC ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS M:56 , ASP M:70BINDING SITE FOR RESIDUE ZN M1503
02AC2SOFTWAREARG M:205 , HOH M:2364 , HOH M:2764 , HOH M:2765 , HOH M:2766 , HOH M:2767 , HOH M:2768BINDING SITE FOR RESIDUE SO4 M1504
03AC3SOFTWARELYS M:108 , ARG M:111 , HOH M:2213 , HOH M:2292 , HOH M:2769 , HOH M:2770BINDING SITE FOR RESIDUE SO4 M1505
04AC4SOFTWAREARG M:259 , GLN M:333 , SO4 M:1511 , HOH M:2771 , HOH M:2773 , HOH M:2787BINDING SITE FOR RESIDUE SO4 M1506
05AC5SOFTWAREGLN M:7 , GLU M:8 , ASN M:9 , HOH M:2009 , HOH M:2774 , HOH M:2775 , HOH M:2776 , HOH M:2777 , HOH M:2778BINDING SITE FOR RESIDUE SO4 M1507
06AC6SOFTWAREHIS M:270 , ARG M:277 , HOH M:2779 , HOH M:2780 , HOH M:2781 , HOH M:2782BINDING SITE FOR RESIDUE SO4 M1508
07AC7SOFTWAREARG M:109 , VAL M:113 , GLU M:173 , HOH M:2204 , HOH M:2783 , HOH M:2784BINDING SITE FOR RESIDUE SO4 M1509
08AC8SOFTWAREASN M:60 , HIS M:66 , NAG M:961 , HOH M:2785BINDING SITE FOR RESIDUE SO4 M1510
09AC9SOFTWAREARG M:194 , ARG M:259 , SO4 M:1506 , HOH M:2760 , HOH M:2771 , HOH M:2786 , HOH M:2787 , HOH M:2788 , HOH M:2789BINDING SITE FOR RESIDUE SO4 M1511
10ACTAUTHORGLN M:187 , GLU M:409 , TYR M:330 , GLU M:464 , GLN M:39 , HIS M:141 , ASN M:186 , TRP M:457GLUCOSE BINDING SUBSITE OF THE ACTIVE SITE
11ASCAUTHORARG M:259 , GLN M:187 , ILE M:257 , PHE M:331 , PHE M:371 , PHE M:473 , TYR M:330ASCORBATE BINDING SITE
12BC1SOFTWAREGLN M:187 , ILE M:257 , ARG M:259 , TYR M:330 , PHE M:331 , PHE M:473 , HOH M:2405 , HOH M:2546 , HOH M:2755 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2759 , HOH M:2760 , HOH M:2761 , HOH M:2762BINDING SITE FOR RESIDUE ASC M 995
13BC2SOFTWAREGLN M:39 , HIS M:141 , ASN M:186 , GLN M:187 , GLU M:409 , TRP M:457 , GLU M:464 , PHE M:465 , HOH M:2756 , HOH M:2763BINDING SITE FOR RESIDUE GOL M1502
14BC3SOFTWAREASN M:316 , LEU M:317 , HOH M:2375 , HOH M:2377 , HOH M:2473 , HOH M:2790 , HOH M:2791 , HOH M:2792BINDING SITE FOR RESIDUE GOL M1512
15BC4SOFTWAREILE M:50 , PHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2290 , HOH M:2296 , HOH M:2793BINDING SITE FOR RESIDUE GOL M1513
16BC5SOFTWAREHIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2396 , HOH M:2732 , HOH M:2794 , HOH M:2795 , HOH M:2796BINDING SITE FOR RESIDUE GOL M1514
17BC6SOFTWAREGLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2797BINDING SITE FOR RESIDUE GOL M1515
18BC7SOFTWARETHR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:2041 , HOH M:2700 , HOH M:2701 , HOH M:2702BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 21 RESIDUES 901 TO 901
19BC8SOFTWARETYR M:58 , ASN M:60 , SER M:213 , SO4 M:1510 , HOH M:2112 , HOH M:2751 , HOH M:2752BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 60 RESIDUES 961 TO 961
20BC9SOFTWAREASN M:90 , SER M:500 , MAN M:957 , HOH M:2703 , HOH M:2705 , HOH M:2706BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 90 RESIDUES 911 TO 911
21CC1SOFTWARESER M:207 , ASN M:218 , THR M:221 , HOH M:2707 , HOH M:2708 , HOH M:2709 , HOH M:2710 , HOH M:2712 , HOH M:2714BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
22CC2SOFTWARELYS M:165 , LEU M:240 , ASN M:244 , HOH M:2379BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 244 RESIDUES 931 TO 931
23CC3SOFTWAREASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , HOH M:2417 , HOH M:2474 , HOH M:2717 , HOH M:2719 , HOH M:2720 , HOH M:2721 , HOH M:2722 , HOH M:2723 , HOH M:2724 , HOH M:2725BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
24CC4SOFTWARETHR 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:1515 , HOH M:2260 , HOH M:2335 , HOH M:2436 , HOH M:2439 , HOH M:2727 , HOH M:2728 , HOH M:2729 , HOH M:2731 , HOH M:2732 , HOH M:2733 , HOH M:2734 , HOH M:2735 , HOH M:2736 , HOH M:2737 , HOH M:2739 , HOH M:2742 , HOH M:2743 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2747 , HOH M:2748 , HOH M:2749 , HOH M:2750 , HOH M:2795BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957
25CC5SOFTWAREASN M:346 , HOH M:2513 , HOH M:2753BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 346 RESIDUES 971 TO 971
26CC6SOFTWAREASN M:482 , ASP M:485 , HOH M:2676BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 482 RESIDUES 991 TO 991
27ZNBAUTHORHIS M:56 , ASP M:70ZN BINDING SITE TOGETHER WITH THE SYMMETRY-RELATED EQUIVALENTS.

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E71)

(-) PROSITE Motifs  (2, 2)

Asymmetric 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
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F1_2PS00653 Glycosyl hydrolases family 1 N-terminal signature.MYRA_SINAL29-43  2M:29-43
2GLYCOSYL_HYDROL_F1_1PS00572 Glycosyl hydrolases family 1 active site.MYRA_SINAL405-413  2M:405-413

(-) Exons   (0, 0)

(no "Exon" information available for 1E71)

(-) Sequences/Alignments

Asymmetric 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 d1e71m_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e71M00 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
                 1e71 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)
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  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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E71)

(-) Gene Ontology  (8, 8)

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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  1e71
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  MYRA_SINAL | P29736
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  3.2.1.147
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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 1e72 1e73 1myr 1w9b 1w9d 2wxd

(-) Related Entries Specified in the PDB File

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
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