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(-) Description

Title :  MYROSINASE FROM SINAPIS ALBA
 
Authors :  W. P. Burmeister, R. Iori, S. Palmieri, B. Henrissat
Date :  23 Mar 97  (Deposition) - 16 Jun 97  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Family 1 Glycosyl Hydrolase, Glucosinolate, Myrosinase, Tim Barrel, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Burmeister, S. Cottaz, H. Driguez, R. Iori, S. Palmieri, B. Henrissat
The Crystal Structures Of Sinapis Alba Myrosinase And A Covalent Glycosyl-Enzyme Intermediate Provide Insights Into The Substrate Recognition And Active-Site Machinery Of An S-Glycosidase.
Structure V. 5 663 1997
PubMed-ID: 9195886  |  Reference-DOI: 10.1016/S0969-2126(97)00221-9

(-) Compounds

Molecule 1 - MYROSINASE
    Cell: MYROSIN CELLS
    Cellular Location: MYROSIN GRAINS
    Chains: A
    EC Number: 3.2.3.1
    Organ: SEED
    Organism Common: WHITE MUSTARD
    Organism Scientific: SINAPIS ALBA
    Organism Taxid: 3728
    Strain: EMERGO
    Synonym: THIOGLUCOSIDE GLUCOHYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 36)

Asymmetric Unit (9, 36)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL4Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7SO410Ligand/IonSULFATE ION
8XYP2Ligand/IonBETA-D-XYLOPYRANOSE
9ZN1Ligand/IonZINC ION
Biological Unit 1 (8, 70)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC4Ligand/IonALPHA-L-FUCOSE
3GOL8Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG24Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
7SO420Ligand/IonSULFATE ION
8XYP4Ligand/IonBETA-D-XYLOPYRANOSE
9ZN-1Ligand/IonZINC ION

(-) Sites  (38, 38)

Asymmetric Unit (38, 38)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:17 , ASP A:18 , GLY A:19 , ASN A:21 , SER A:24 , HOH A:1008 , HOH A:1153 , HOH A:1404BINDING SITE FOR RESIDUE NAG A 901
02AC2SOFTWAREASN A:90 , SER A:500 , MAN A:957 , HOH A:1039 , HOH A:1419BINDING SITE FOR RESIDUE NAG A 911
03AC3SOFTWARESER A:207 , ASN A:218 , THR A:221 , NAG A:923 , HOH A:1121 , HOH A:1582 , HOH A:1651BINDING SITE FOR RESIDUE NAG A 921
04AC4SOFTWAREARG A:306 , NAG A:921BINDING SITE FOR RESIDUE NAG A 923
05AC5SOFTWARELYS A:165 , ASP A:239 , LEU A:240 , ASN A:244BINDING SITE FOR RESIDUE NAG A 931
06AC6SOFTWAREASN A:265 , ASP A:268 , ALA A:362 , FUC A:942 , NAG A:943 , HOH A:1184 , HOH A:1586 , HOH A:1619 , HOH A:1650BINDING SITE FOR RESIDUE NAG A 941
07AC7SOFTWARENAG A:941 , NAG A:943 , SO4 A:1002 , HOH A:1619BINDING SITE FOR RESIDUE FUC A 942
08AC8SOFTWAREASN A:316 , NAG A:941 , FUC A:942 , BMA A:944 , XYP A:945 , HOH A:1434 , HOH A:1450 , HOH A:1549 , HOH A:1610 , HOH A:1619 , HOH A:1675BINDING SITE FOR RESIDUE NAG A 943
09AC9SOFTWARENAG A:943 , XYP A:945 , HOH A:1450BINDING SITE FOR RESIDUE BMA A 944
10ASNAUTHORGLU A:409 , GLN A:187ACTIVE SITE NUCLEOPHILE AT THE POSITION OF THE GENERAL ACID/BASE
11BC1SOFTWAREASN A:316 , LYS A:319 , NAG A:943 , BMA A:944 , HOH A:1450 , HOH A:1644BINDING SITE FOR RESIDUE XYP A 945
12BC2SOFTWAREASN A:292 , THR A:294 , FUC A:952 , NAG A:953 , HOH A:1049 , HOH A:1177 , HOH A:1178 , HOH A:1290BINDING SITE FOR RESIDUE NAG A 951
13BC3SOFTWAREILE A:129 , GLN A:297 , NAG A:951 , NAG A:953 , HOH A:1056 , HOH A:1244 , HOH A:1290 , HOH A:1335 , HOH A:1448BINDING SITE FOR RESIDUE FUC A 952
14BC4SOFTWAREGLN A:297 , NAG A:951 , FUC A:952 , BMA A:954 , XYP A:955 , MAN A:956 , GOL A:1006 , HOH A:1179 , HOH A:1347 , HOH A:1446 , HOH A:1461 , HOH A:1597 , HOH A:1667BINDING SITE FOR RESIDUE NAG A 953
15BC5SOFTWAREGLY A:132 , NAG A:953 , XYP A:955 , MAN A:956 , MAN A:957 , GOL A:1006 , HOH A:1543 , HOH A:1667 , HOH A:1669BINDING SITE FOR RESIDUE BMA A 954
16BC6SOFTWARENAG A:953 , BMA A:954 , MAN A:956 , HOH A:1643 , HOH A:1667 , HOH A:1671BINDING SITE FOR RESIDUE XYP A 955
17BC7SOFTWAREGLN A:297 , NAG A:953 , BMA A:954 , XYP A:955 , HOH A:1420 , HOH A:1461 , HOH A:1631 , HOH A:1632BINDING SITE FOR RESIDUE MAN A 956
18BC8SOFTWAREASN A:90 , THR A:92 , NAG A:911 , BMA A:954 , HOH A:1426BINDING SITE FOR RESIDUE MAN A 957
19BC9SOFTWAREASN A:346BINDING SITE FOR RESIDUE NDG A 971
20CC1SOFTWARETYR A:264 , ASN A:265 , ASP A:266 , ASN A:361 , SER A:363 , HIS A:365 , NAG A:983 , HOH A:1328 , HOH A:1546 , HOH A:1674BINDING SITE FOR RESIDUE NAG A 981
21CC2SOFTWAREPRO A:11 , NAG A:981 , HOH A:1674BINDING SITE FOR RESIDUE NAG A 983
22CC3SOFTWAREASN A:482 , ASP A:485 , HOH A:1504BINDING SITE FOR RESIDUE NAG A 991
23CC4SOFTWAREHIS A:56 , ASP A:70BINDING SITE FOR RESIDUE ZN A 992
24CC5SOFTWAREARG A:205 , HOH A:1146 , HOH A:1276 , HOH A:1522 , HOH A:1535BINDING SITE FOR RESIDUE SO4 A 993
25CC6SOFTWARELYS A:108 , ARG A:111 , HOH A:1144 , HOH A:1519BINDING SITE FOR RESIDUE SO4 A 994
26CC7SOFTWAREARG A:259 , GLN A:333 , LEU A:357 , SO4 A:1000 , HOH A:1082 , HOH A:1483 , HOH A:1532BINDING SITE FOR RESIDUE SO4 A 995
27CC8SOFTWAREGLN A:7 , GLU A:8 , ASN A:9 , HOH A:1316 , HOH A:1401 , HOH A:1412 , HOH A:1621 , HOH A:1661BINDING SITE FOR RESIDUE SO4 A 996
28CC9SOFTWAREHIS A:270 , ALA A:273 , ARG A:277 , HOH A:1045 , HOH A:1424 , HOH A:1555BINDING SITE FOR RESIDUE SO4 A 997
29DC1SOFTWAREARG A:109 , VAL A:113 , LEU A:170 , GLU A:173 , HOH A:1510 , HOH A:1571 , HOH A:1576BINDING SITE FOR RESIDUE SO4 A 998
30DC2SOFTWAREASP A:60 , HIS A:66BINDING SITE FOR RESIDUE SO4 A 999
31DC3SOFTWAREARG A:194 , ARG A:259 , SO4 A:995 , HOH A:1094 , HOH A:1344 , HOH A:1483 , HOH A:1532 , HOH A:1589BINDING SITE FOR RESIDUE SO4 A 1000
32DC4SOFTWAREASP A:239 , ARG A:269 , ASN A:316 , LEU A:317 , HOH A:1026 , HOH A:1339BINDING SITE FOR RESIDUE SO4 A 1001
33DC5SOFTWARETYR A:427 , LYS A:490 , FUC A:942BINDING SITE FOR RESIDUE SO4 A 1002
34DC6SOFTWAREPHE A:54 , ARG A:57 , GLN A:146 , GLN A:149 , PRO A:203 , TYR A:215 , HOH A:1277 , HOH A:1308BINDING SITE FOR RESIDUE GOL A 1003
35DC7SOFTWAREHIS A:247 , GLY A:249 , GLN A:280 , GLN A:297 , ILE A:298 , HOH A:1035 , HOH A:1290 , HOH A:1335 , HOH A:1453BINDING SITE FOR RESIDUE GOL A 1004
36DC8SOFTWAREGLN A:39 , HIS A:141 , ASN A:186 , GLN A:187 , GLU A:409 , TRP A:457 , GLU A:464 , PHE A:465 , HOH A:1478BINDING SITE FOR RESIDUE GOL A 1005
37DC9SOFTWAREGLY A:132 , THR A:134 , NAG A:953 , BMA A:954 , HOH A:1166 , HOH A:1338 , HOH A:1446 , HOH A:1593BINDING SITE FOR RESIDUE GOL A 1006
38ZNBAUTHORHIS A:56 , ASP A:70ZN BINDING SITE TOGETHER WITH THE SYMMETRY- RELATED EQUIVALENTS.

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MYR)

(-) 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 A 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 d1myra_ A: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1myrA00 A:3-501 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------Glyco_hydro_1-1myrA01 A:21-501                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author ...................hhh.....eeeee..hhhh.........hhhhhhhh.hhhh............hhhhhhhhhhhhhhh...eeeee..hhhh.....hhh...hhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh.hhh.hhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhhh.hhh..eee.eeee.eeee.....hhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhh.....hhhhhhh......eeeee..eeeeee...........hhhhh.eeee...................hhh.....hhhhhhhhhhhhhh....eeeeee..........hhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeeeee...................eeee..eeeeeee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1myr A   3 EITCQENNPFTCGNTDGLNSSSFEADFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPDKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNQKGIDYYHGLIDGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKQFFLGWFMGPLTNGTYPQIMIDTVGARLPTFSPEETNLVKGSYDFLGLNYYFTQYAQPSPNPVNATNHTAMMDAGAKLTYINASGHYIGPLFESDGGDGSSNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGSENRKESMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNNGFTVRFGLSYINWNNVTDRDLKKSGQWYQKFISP 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  (1, 1)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  1myr
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  MYRA_SINAL | P29736
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MYRA_SINAL | P29736
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 1w9b 1w9d 2wxd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MYR)