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(-) Description

Title :  MYROSINASE FROM SINAPIS ALBA WITH THE BOUND TRANSITION STATE ANALOGUE GLUCO-TETRAZOLE
 
Authors :  W. P. Burmeister
Date :  22 Aug 00  (Deposition) - 05 Jan 01  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  M
Biol. Unit 1:  M  (2x)
Keywords :  Hydrolase, Family 1 Glycosyl Hydrolase, Glucosinolate, Tim Barrel, D-Glucono-1, 5-Lactone, Transition State (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: 3.2.3.1
    Organ: SEED
    Organism Common: WHITE MUSTARD
    Organism Scientific: SINAPIS ALBA
    Organism Taxid: 3728
    Strain: EMERGO
    Synonym: THIOGLUCOSIDE GLUCOHYDROLASE, SINIGRINASE, THIOGLUCOSIDASE

 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, 33)

Asymmetric Unit (9, 33)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL4Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NTZ1Ligand/IonNOJIRIMYCINE TETRAZOLE
7SO47Ligand/IonSULFATE ION
8XYP2Ligand/IonBETA-D-XYLOPYRANOSE
9ZN1Ligand/IonZINC ION
Biological Unit 1 (8, 64)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC4Ligand/IonALPHA-L-FUCOSE
3GOL8Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NTZ2Ligand/IonNOJIRIMYCINE TETRAZOLE
7SO414Ligand/IonSULFATE ION
8XYP4Ligand/IonBETA-D-XYLOPYRANOSE
9ZN-1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG M:205 , HOH M:2368 , HOH M:2763 , HOH M:2764 , HOH M:2765 , HOH M:2766BINDING SITE FOR RESIDUE SO4 M1513
02AC2SOFTWARELYS M:108 , ARG M:111 , HOH M:2216 , HOH M:2291 , HOH M:2767 , HOH M:2768BINDING SITE FOR RESIDUE SO4 M1514
03AC3SOFTWAREARG M:259 , GLN M:333 , HOH M:2769 , HOH M:2770 , HOH M:2771 , HOH M:2772 , HOH M:2774BINDING SITE FOR RESIDUE SO4 M1515
04AC4SOFTWAREGLN M:7 , GLU M:8 , ASN M:9 , HOH M:2011 , HOH M:2775 , HOH M:2776 , HOH M:2777 , HOH M:2778 , HOH M:2779BINDING SITE FOR RESIDUE SO4 M1516
05AC5SOFTWAREHIS M:270 , ALA M:273 , ARG M:277 , HOH M:2424 , HOH M:2780 , HOH M:2781 , HOH M:2782BINDING SITE FOR RESIDUE SO4 M1517
06AC6SOFTWAREARG M:109 , VAL M:113 , GLU M:173 , HOH M:2208 , HOH M:2783 , HOH M:2784BINDING SITE FOR RESIDUE SO4 M1518
07AC7SOFTWAREASN M:60 , HIS M:66 , NAG M:961 , HOH M:2785BINDING SITE FOR RESIDUE SO4 M1519
08AC8SOFTWAREHIS M:56 , ASP M:70BINDING SITE FOR RESIDUE ZN M1520
09AC9SOFTWAREGLN 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 , HOH M:2751 , HOH M:2752 , HOH M:2753BINDING SITE FOR RESIDUE NTZ M 999
10BC1SOFTWAREILE 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:2754 , HOH M:2755BINDING SITE FOR RESIDUE GOL M1502
11BC2SOFTWAREHIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:2756 , HOH M:2757 , HOH M:2758 , HOH M:2759 , HOH M:2760BINDING SITE FOR RESIDUE GOL M1503
12BC3SOFTWAREGLY M:132 , THR M:134 , NAG M:953 , BMA M:954 , HOH M:2271 , HOH M:2761BINDING SITE FOR RESIDUE GOL M1504
13BC4SOFTWAREASN M:316 , LEU M:317 , HOH M:2379 , HOH M:2388 , HOH M:2721 , HOH M:2786 , HOH M:2787 , HOH M:2788BINDING SITE FOR RESIDUE GOL M1534
14BC5SOFTWARETHR M:17 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:2700 , HOH M:2701BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 21 RESIDUES 901 TO 901
15BC6SOFTWARETYR M:58 , ASN M:60 , SER M:213 , SO4 M:1519 , HOH M:2108 , HOH M:2114 , HOH M:2748BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 60 RESIDUES 961 TO 961
16BC7SOFTWAREASN M:90 , SER M:500 , HOH M:2702 , HOH M:2703 , HOH M:2704BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 90 RESIDUES 911 TO 911
17BC8SOFTWARESER M:207 , ASN M:218 , THR M:221 , HOH M:2705 , HOH M:2706 , HOH M:2707 , HOH M:2708 , HOH M:2710 , HOH M:2712BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 218 RESIDUES 921 TO 923
18BC9SOFTWARELYS M:165 , LEU M:240 , ASN M:244 , HOH M:2381BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 244 RESIDUES 931 TO 931
19CC1SOFTWAREASN M:265 , ASP M:268 , ASN M:316 , LYS M:319 , ALA M:362 , HOH M:2421 , HOH M:2479 , HOH M:2714 , HOH M:2715 , HOH M:2716 , HOH M:2718 , HOH M:2719 , HOH M:2720 , HOH M:2721 , HOH M:2722 , HOH M:2723BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 265 RESIDUES 941 TO 945
20CC2SOFTWARETHR M:92 , ILE M:129 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , GOL M:1504 , HOH M:2260 , HOH M:2332 , HOH M:2443 , HOH M:2445 , HOH M:2726 , HOH M:2727 , HOH M:2729 , HOH M:2730 , HOH M:2731 , HOH M:2732 , HOH M:2733 , HOH M:2734 , HOH M:2735 , HOH M:2738 , HOH M:2739 , HOH M:2740 , HOH M:2741 , HOH M:2742 , HOH M:2743 , HOH M:2744 , HOH M:2745 , HOH M:2746 , HOH M:2747 , HOH M:2757 , HOH M:2759BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 292 RESIDUES 951 TO 957
21CC3SOFTWAREASN M:346BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 346 RESIDUES 971 TO 971
22CC4SOFTWAREASN M:482 , ASP M:485 , HOH M:2676BINDING SITE FOR CHAIN M OF SUGAR BOUND TO ASN M 482 RESIDUES 991 TO 991

(-) 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 1E6Q)

(-) 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 1E6Q)

(-) 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 d1e6qm_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e6qM00 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
                 1e6q 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 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 1E6Q)

(-) 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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  1e6q
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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 1e6s 1e6x 1e70 1e71 1e72 1e73 1myr 1w9b 1w9d 2wxd

(-) Related Entries Specified in the PDB File

1e4m MYROSINASE FROM SINAPIS ALBA
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
1myr MYROSINASE FROM SINAPIS ALBA
2myr MYROSINASE, 2-DEOXY-2-FLUORO-GLUCOSYL ENZYME