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(-) Description

Title :  STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 2: STRUCTURE AFTER IRRADIATION WITH 9.1*10E15 PHOTONS/MM2
 
Authors :  W. P. Burmeister
Date :  05 Dec 99  (Deposition) - 03 Mar 00  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  M
Biol. Unit 1:  M  (2x)
Keywords :  Hydrolase, Glycosidase, Radiation Damage, Radiolysis, Cryo-Cooled (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. P. Burmeister
Structural Changes In A Cryo-Cooled Protein Crystal Due To Radiation Damage
Acta Crystallogr. , Sect. D V. 56 328 2000
PubMed-ID: 10713520  |  Reference-DOI: 10.1107/S0907444999016261
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MYROSINASE MA1
    Cell: MYROSIN CELLS
    Cellular Location: MYROSIN GRAINS
    Chains: M
    EC Number: 3.2.1.147
    Fragment: RESIDUES 3-501
    Organ: SEED
    Organism Common: WHITE MUSTARD
    Organism Scientific: SINAPIS ALBA
    Organism Taxid: 3728
    Other Details: AFTER IRRADIATION WITH 9.1*10E15 PHOTONS/MM2 OF PHOTONS
    Strain: EMERGO
    Synonym: SINIGRINASE, THIOGLUCOSIDASE, THIOGLUCOSIDE GLUCOHYDROLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 36)

Asymmetric Unit (8, 36)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GOL5Ligand/IonGLYCEROL
4MAN2Ligand/IonALPHA-D-MANNOSE
5NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO48Ligand/IonSULFATE ION
7XYP2Ligand/IonBETA-D-XYLOPYRANOSE
8ZN1Ligand/IonZINC ION
Biological Unit 1 (7, 70)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC4Ligand/IonALPHA-L-FUCOSE
3GOL10Ligand/IonGLYCEROL
4MAN4Ligand/IonALPHA-D-MANNOSE
5NAG28Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO416Ligand/IonSULFATE ION
7XYP4Ligand/IonBETA-D-XYLOPYRANOSE
8ZN-1Ligand/IonZINC ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS M:56 , ASN M:68 , ASP M:70BINDING SITE FOR RESIDUE ZN M 1524
02AC2SOFTWAREARG M:106 , ARG M:205 , HOH M:2192 , HOH M:2213 , HOH M:2356 , HOH M:3002 , HOH M:3003 , HOH M:3004BINDING SITE FOR RESIDUE SO4 M 1525
03AC3SOFTWARELYS M:108 , ARG M:111 , GLU M:151 , HOH M:2209 , HOH M:2292 , HOH M:3005 , HOH M:3006BINDING SITE FOR RESIDUE SO4 M 1526
04AC4SOFTWAREGLN M:7 , GLU M:8 , ASN M:9 , HOH M:2004 , HOH M:3010 , HOH M:3011 , HOH M:3012 , HOH M:3013 , HOH M:3014 , HOH M:3015BINDING SITE FOR RESIDUE SO4 M 1528
05AC5SOFTWAREHIS M:270 , ALA M:273 , ARG M:277 , HOH M:2413 , HOH M:3016 , HOH M:3017BINDING SITE FOR RESIDUE SO4 M 1529
06AC6SOFTWAREARG M:109 , VAL M:113 , GLU M:173 , HOH M:2202 , HOH M:3018 , HOH M:3019BINDING SITE FOR RESIDUE SO4 M 1530
07AC7SOFTWAREASN M:60 , HIS M:66 , NAG M:1519 , HOH M:3020BINDING SITE FOR RESIDUE SO4 M 1531
08AC8SOFTWAREASN M:316 , LEU M:317 , HOH M:1032 , HOH M:2472 , HOH M:3026 , HOH M:3027 , HOH M:3028 , HOH M:3029BINDING SITE FOR RESIDUE GOL M 1533
09AC9SOFTWAREPHE M:54 , ARG M:57 , GLN M:146 , GLN M:149 , PRO M:203 , TYR M:215 , HOH M:2354 , HOH M:3030 , HOH M:3031BINDING SITE FOR RESIDUE GOL M 1534
10BC1SOFTWAREHIS M:247 , GLY M:249 , GLU M:280 , GLN M:297 , ILE M:298 , HOH M:1040 , FUC M:1513 , HOH M:2385 , HOH M:2426 , HOH M:3032 , HOH M:3033 , HOH M:3034BINDING SITE FOR RESIDUE GOL M 1535
11BC2SOFTWAREGLY M:132 , THR M:134 , NAG M:1514 , BMA M:1515 , HOH M:3035BINDING SITE FOR RESIDUE GOL M 1536
12BC3SOFTWAREGLN 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:2482BINDING SITE FOR RESIDUE GOL M 1537
13BC4SOFTWARETHR M:17 , ASP M:18 , ALA M:19 , ASN M:21 , SER M:24 , PRO M:501 , HOH M:1010 , HOH M:1011 , HOH M:1012Binding site for Mono-Saccharide NAG M1502 bound to ASN M 21
14BC5SOFTWARETYR M:58 , ASN M:60 , HOH M:1056 , HOH M:1057 , HOH M:1059 , SO4 M:1531 , HOH M:2085 , HOH M:2106Binding site for Mono-Saccharide NAG M1519 bound to ASN M 60
15BC6SOFTWAREASN M:90 , SER M:500 , HOH M:1013 , HOH M:1016 , HOH M:2686Binding site for Mono-Saccharide NAG M1503 bound to ASN M 90
16BC7SOFTWARESER M:207 , ASN M:218 , THR M:221 , GLU M:305 , HOH M:1017 , HOH M:1019 , HOH M:1020 , HOH M:1021 , HOH M:1022Binding site for Poly-Saccharide residues NAG M1504 through NAG M1505 bound to ASN M 218
17BC8SOFTWARELYS M:165 , LEU M:240 , ASN M:244 , HOH M:1025 , HOH M:2371Binding site for Mono-Saccharide NAG M1506 bound to ASN M 244
18BC9SOFTWAREASN M:265 , ASP M:268 , ALA M:362 , HOH M:1026 , HOH M:1027 , HOH M:1028 , HOH M:1029 , HOH M:1030 , HOH M:1031 , HOH M:1032 , HOH M:1033 , HOH M:1034 , HOH M:2410 , HOH M:2613 , HOH M:2615Binding site for Poly-Saccharide residues NAG M1507 through XYP M1511 bound to ASN M 265
19CC1SOFTWARETHR M:92 , LYS M:180 , ASN M:292 , THR M:294 , GLN M:297 , ILE M:300 , HOH M:1035 , HOH M:1036 , HOH M:1037 , HOH M:1038 , HOH M:1040 , HOH M:1041 , HOH M:1044 , HOH M:1045 , HOH M:1047 , HOH M:1048 , HOH M:1050 , HOH M:1051 , HOH M:1052 , HOH M:1053 , HOH M:1055 , GOL M:1535 , GOL M:1536 , HOH M:2322 , HOH M:2432 , HOH M:3033 , HOH M:3036Binding site for Poly-Saccharide residues NAG M1512 through MAN M1518 bound to ASN M 292
20CC2SOFTWAREASN M:346 , HOH M:2504Binding site for Mono-Saccharide NAG M1520 bound to ASN M 346
21CC3SOFTWAREPRO M:11 , PHE M:12 , THR M:13 , ASN M:265 , ASP M:266 , ASN M:361 , SER M:363 , HIS M:365 , HOH M:1060 , HOH M:1061 , HOH M:1062 , HOH M:1063 , HOH M:2025 , HOH M:2400 , HOH M:2404 , HOH M:2406 , HOH M:2485Binding site for Poly-Saccharide residues NAG M1521 through NAG M1522 bound to ASN M 361
22CC4SOFTWAREASN M:482 , ASP M:485 , HOH M:2666Binding site for Mono-Saccharide NAG M1523 bound to ASN M 482
23CC5SOFTWAREARG M:194 , ARG M:259 , GLN M:333 , HOH M:2332 , HOH M:3007 , HOH M:3009 , HOH M:3021 , HOH M:3022 , HOH M:3023 , HOH M:3024Binding site for residues SO4 M1527 and SO4 M1532

(-) 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 1DWF)

(-) 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 1DWF)

(-) 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 d1dwfm_ M: Plant beta-glucosidase (myrosinase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1dwfM00 M:3-501 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh....eeeee.hhhhhh.......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee.eeee.eeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh.....eeeee..eeeeee..........hhhhhh.eeee..................hhhhh....hhhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..................eeee..eeeeeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------GLYCOSYL_HYDROL-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_---------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dwf M   3 EITCQENLPFTCGNTDALNSSSFSSDFIFGVASSAYQIEGTIGRGLNIWDGFTHRYPNKSGPDHGNGDTTCDSFSYWQKDIDVLDELNATGYRFSIAWSRIIPRGKRSRGVNEKGIDYYHGLISGLIKKGITPFVTLFHWDLPQTLQDEYEGFLDPQIIDDFKDYADLCFEEFGDSVKYWLTINQLYSVPTRGYGSALDAPGRCSPTVDPSCYAGNSSTEPYIVAHHQLLAHAKVVDLYRKNYTHQGGKIGPTMITRWFLPYNDTDRHSIAATERMKEFFLGWFMGPLTNGTYPQIMIDTVGERLPSFSPEESNLVKGSYDFLGLNYYFTQYAQPSPNPVNSTNHTAMMDAGAKLTYINASGHYIGPLFEKDKADSTDNIYYYPKGIYSVMDYFKNKYYNPLIYVTENGISTPGDENRNQSMLDYTRIDYLCSHLCFLNKVIKEKDVNVKGYLAWALGDNYEFNKGFTVRFGLSYIDWNNVTDRDLKKSGQWYQTFISP 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 1DWF)

(-) 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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  1dwf
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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 1dwg 1dwh 1dwi 1dwj 1e4m 1e6q 1e6s 1e6x 1e70 1e71 1e72 1e73 1myr 1w9b 1w9d 2wxd

(-) Related Entries Specified in the PDB File

1dwa STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 1: STRUCTURE PRIOR TO IRRADIATION
1dwg STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL: PART 3: STRUCTURE AFTER IRRADIATION WITH 18.2*10E15 PHOTONS/MM2.
1dwh STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 4: STRUCTURE AFTER IRRADIATION WITH 27.2*10E15 PHOTONS/MM2
1dwi STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. PART 5: STRUCTURE AFTER IRRADIATION WITH 54.0*10E15 PHOTONS/MM2
1dwj STUDY ON RADIATION DAMAGE ON A CRYOCOOLED CRYSTAL. REFINED PART 6: STRUCTURE AFTER A RADIATION DOSE OF 54*10E15 PHOTONS/MM2
1myr MYROSINASE FROM SINAPIS ALBA