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(-) Description

Title :  CRYSTAL STRUCTURE OF RICE ALPHA-GALACTOSIDASE
 
Authors :  Z. Fujimoto, S. Kaneko, M. Momma, H. Kobayashi, H. Mizuno
Date :  18 Mar 03  (Deposition) - 01 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim-Barrel, Beta-Alpha-Barrel, Greek Key Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Fujimoto, S. Kaneko, M. Momma, H. Kobayashi, H. Mizuno
Crystal Structure Of Rice Alpha-Galactosidase Complexed Wit D-Galactose
J. Biol. Chem. V. 278 20313 2003
PubMed-ID: 12657636  |  Reference-DOI: 10.1074/JBC.M302292200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIUDES 1-362
    Organism Common: RICE
    Organism Scientific: ORYZA SATIVA
    Organism Taxid: 4530

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1GLA1Ligand/IonALPHA D-GALACTOSE
2GOL7Ligand/IonGLYCEROL
3PT1Ligand/IonPLATINUM (II) ION
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:16 , ASP A:51 , ASP A:52 , TYR A:93 , CYS A:101 , LYS A:128 , ASP A:130 , CYS A:162 , TRP A:164 , ARG A:181 , ASP A:185 , MET A:217 , HOH A:1615 , HOH A:1773 , HOH A:1829 , HOH A:2010BINDING SITE FOR RESIDUE GLA A 1501
02AC2SOFTWARETHR A:183 , GLY A:184 , ARG A:196 , GLU A:199 , HOH A:2000 , HOH A:2170BINDING SITE FOR RESIDUE SO4 A 701
03AC3SOFTWAREMET A:140 , TRP A:172 , MET A:176 , HOH A:1701 , HOH A:2047BINDING SITE FOR RESIDUE PT A 801
04AC4SOFTWARESER A:98 , LEU A:109 , ASP A:110 , ARG A:137 , THR A:329 , HOH A:1619 , HOH A:1745 , HOH A:1771 , HOH A:1809BINDING SITE FOR RESIDUE GOL A 1601
05AC5SOFTWARETYR A:57 , SER A:98 , GLN A:99 , PRO A:106 , HOH A:1642 , HOH A:1675 , HOH A:1717 , HOH A:1729 , HOH A:1809BINDING SITE FOR RESIDUE GOL A 1602
06AC6SOFTWARETRP A:190 , THR A:194 , ARG A:306 , HOH A:1823 , HOH A:1928 , HOH A:1942 , HOH A:2202BINDING SITE FOR RESIDUE GOL A 1603
07AC7SOFTWAREALA A:170 , TRP A:172 , ALA A:173 , GLY A:174 , TYR A:206 , SER A:308 , TYR A:309 , HOH A:1680 , HOH A:1692 , HOH A:1858BINDING SITE FOR RESIDUE GOL A 1604
08AC8SOFTWARETYR A:206 , SER A:226 , GLU A:229 , PRO A:351 , HIS A:352 , HOH A:1766 , HOH A:2217BINDING SITE FOR RESIDUE GOL A 1605
09AC9SOFTWAREGLU A:30 , ASP A:110 , GLU A:112 , GLU A:113 , ARG A:145 , HOH A:1651 , HOH A:1661 , HOH A:1902BINDING SITE FOR RESIDUE GOL A 1606
10BC1SOFTWARETHR A:8 , PRO A:9 , GLN A:10 , MET A:11 , GLY A:44 , GLN A:46 , TYR A:47 , GLN A:271 , HOH A:1698 , HOH A:2039 , HOH A:2220BINDING SITE FOR RESIDUE GOL A 1607

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:53
2A:101 -A:132

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UAS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.AGAL_ORYSJ99-115  1A:44-60

(-) Exons   (0, 0)

(no "Exon" information available for 1UAS)

(-) 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 A from PDB  Type:PROTEIN  Length:362
 aligned with AGAL_ORYSJ | Q9FXT4 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:362
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415  
           AGAL_ORYSJ    56 FENGLGRTPQMGWNSWNHFYCGINEQIIRETADALVNTGLAKLGYQYVNIDDCWAEYSRDSQGNFVPNRQTFPSGIKALADYVHAKGLKLGIYSDAGSQTCSNKMPGSLDHEEQDVKTFASWGVDYLKYDNCNDAGRSVMERYTRMSNAMKTYGKNIFFSLCEWGKENPATWAGRMGNSWRTTGDIADNWGSMTSRADENDQWAAYAGPGGWNDPDMLEVGNGGMSEAEYRSHFSIWALAKAPLLIGCDVRSMSQQTKNILSNSEVIAVNQDSLGVQGKKVQSDNGLEVWAGPLSNNRKAVVLWNRQSYQATITAHWSNIGLAGSVAVTARDLWAHSSFAAQGQISASVAPHDCKMYVLTPN 417
               SCOP domains d1uasa2 A:1-273 Melibiase                                                                                                                                                                                                                                                        d1uasa1 A:274-362 Melibiase                                                               SCOP domains
               CATH domains 1uasA01 A:1-274 Aldolase class I                                                                                                                                                                                                                                                  1uasA02 A:275-362 Golgi alpha-mannosidase II                                             CATH domains
               Pfam domains Melibiase-1uasA01 A:1-106                                                                                 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh..eee.........................hhhhhhhhhhhh..eeeeeee...............hhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeeee..eeeeeee.....eeeeeee.....eeeeee.hhh......eeeeee....eeeeee.eeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------ALPHA_GALACTOSIDA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uas A   1 FENGLGRTPQMGWNSWNHFYCGINEQIIRETADALVNTGLAKLGYQYVNIDDCWAEYSRDSQGNFVPNRQTFPSGIKALADYVHAKGLKLGIYSDAGSQTCSNKMPGSLDHEEQDVKTFASWGVDYLKYDNCNDAGRSVMERYTRMSNAMKTYGKNIFFSLCEWGKENPATWAGRMGNSWRTTGDIADNWGSMTSRADENDQWAAYAGPGGWNDPDMLEVGNGGMSEAEYRSHFSIWALAKAPLLIGCDVRSMSQQTKNILSNSEVIAVNQDSLGVQGKKVQSDNGLEVWAGPLSNNRKAVVLWNRQSYQATITAHWSNIGLAGSVAVTARDLWAHSSFAAQGQISASVAPHDCKMYVLTPN 362
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGAL_ORYSJ | Q9FXT4)
molecular function
    GO:0004557    alpha-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0052692    raffinose alpha-galactosidase activity    Catalysis of the reaction: raffinose + H2O = alpha-D-galactose + sucrose.
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:0009505    plant-type cell wall    A more or less rigid stucture lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances.

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