Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF ALFA-GALACTOSIDASE (MEL1) FROM SACCHAROMYCES CEREVISIAE
 
Authors :  R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J Aparicio
Date :  11 Feb 10  (Deposition) - 30 Jun 10  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Alpha-Galactosidase, Tetramer, Gh27, Glycoprotein, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Fernandez-Leiro, A. Pereira-Rodriguez, M. E. Cerdan, M. Becerra, J. Sanz-Aparicio
Structural Analysis Of Saccharomyces Cerevisiae Alpha-Galactosidase And Its Complexes With Natural Substrates Reveals New Insights Into Substrate Specificity Of Gh27 Glycosidases.
J. Biol. Chem. V. 285 28020 2010
PubMed-ID: 20592022  |  Reference-DOI: 10.1074/JBC.M110.144584

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE 1
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Plasmid: YEPFLAG1
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Gene: MEL1
    Mutation: YES
    Organism Common: BREWER'S YEAST,LAGER BEER YEAST,YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ALPHA-D-GALACTOSIDE GALACTOHYDROLASE 1, MELIBIASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2GOL3Ligand/IonGLYCEROL
3NA1Ligand/IonSODIUM ION
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 48)
No.NameCountTypeFull Name
1BTB4Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2GOL12Ligand/IonGLYCEROL
3NA-1Ligand/IonSODIUM ION
4NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:82 , HIS A:102 , ASN A:105 , GLU A:133 , HOH A:566 , HOH A:640 , HOH A:655 , HOH A:712 , HOH A:885BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWAREASN A:175 , GLY A:178 , HOH A:628 , HOH A:859BINDING SITE FOR RESIDUE NAG A 2001
03AC3SOFTWAREGLY A:267 , GLY A:269 , ASN A:270 , LEU A:382 , HOH A:487 , HOH A:598 , NAG A:3002BINDING SITE FOR RESIDUE NAG A 3001
04AC4SOFTWAREASN A:298 , HOH A:598 , HOH A:629 , NAG A:3001BINDING SITE FOR RESIDUE NAG A 3002
05AC5SOFTWAREASP A:273 , SER A:302 , ASN A:403 , HOH A:586 , HOH A:588 , HOH A:684 , HOH A:729BINDING SITE FOR RESIDUE NAG A 4001
06AC6SOFTWAREASP A:63 , THR A:417 , ASN A:422 , HOH A:686 , HOH A:805 , NAG A:5002BINDING SITE FOR RESIDUE NAG A 5001
07AC7SOFTWARESER A:107 , HOH A:805 , NAG A:5001BINDING SITE FOR RESIDUE NAG A 5002
08AC8SOFTWARETRP A:328 , TYR A:330 , ASN A:370BINDING SITE FOR RESIDUE NAG A 6001
09AC9SOFTWARETRP A:37 , ASP A:72 , ASP A:73 , CYS A:121 , ALA A:122 , LYS A:147 , ASP A:149 , HOH A:887 , HOH A:888BINDING SITE FOR RESIDUE GOL A 7001
10BC1SOFTWAREASP A:35 , TRP A:37 , ASN A:38 , LYS A:147 , ARG A:205 , VAL A:210 , ASP A:262 , ASN A:263 , HOH A:525 , HOH A:626 , HOH A:868BINDING SITE FOR RESIDUE GOL A 7002
11BC2SOFTWAREMET A:64 , SER A:308 , GLN A:309 , ALA A:310 , ASN A:399 , LEU A:420 , TYR A:421 , HOH A:508BINDING SITE FOR RESIDUE GOL A 7003
12BC3SOFTWAREHIS A:98 , HIS A:102 , BTB A:9001BINDING SITE FOR RESIDUE NA A 8001
13BC4SOFTWAREGLU A:46 , SER A:81 , ASP A:82 , ASN A:94 , HIS A:98 , HIS A:102 , NA A:8001BINDING SITE FOR RESIDUE BTB A 9001

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:42 -A:74
2A:121 -A:151
3A:221 -A:237
4A:223 -A:230

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LRK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LRK)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.MEL1_YEASX65-80  1A:65-80
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.MEL1_YEASX65-80  4A:65-80

(-) Exons   (0, 0)

(no "Exon" information available for 3LRK)

(-) 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:452
 aligned with MEL1_YEASX | P04824 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:452
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468  
           MEL1_YEASX    19 VSPSYNGLGLTPQMGWDNWNTFACDVSEQLLLDTADRISDLGLKDMGYKYIILDDCWSSGRDSDGFLVADEQKFPNGMGHVADHLHNNSFLFGMYSSAGEYTCAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPEISYHRYKAMSDALNKTGRPIFYSLCNWGQDLTFYWGSGIANSWRMSGDVTAEFTRPDSRCPCDGDEYDCKYAGFHCSIMNILNKAAPMGQNAGVGGWNDLDNLEVGVGNLTDDEEKAHFSMWAMVKSPLIIGANVNNLKASSYSIYSQASVIAINQDSNGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALLNGGSVSRPMNTTLEEIFFDSNLGSKKLTSTWDIYDLWANRVDNSTASAILGRNKTATGILYNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPS 470
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Melibiase-3lrkA01 A:19-363                                                                                                                                                                                                                                                                                                                               ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeehhhhhh...hhhhhhhhhhhhhhh.hhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhh...eeee......hhhhhh.....eee................................hhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee..hhhh..hhhhhhh.hhhhhhhhh.......eeeeeee..........eeeeeeee.....eeeeeee.....eeeeehhhhhh......hhhhhh.eeeee......hhhhhhhhhh...............hhhhhhhh.hhhhhheeeeee.....eeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------ALPHA_GALACTOSID------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lrk A  19 VSPSYNGLGLTPQMGWDNWNTFACDVSEQLLLDTADRISDLGLKDMGYKYIILDDCWSSGRDSDGFLVADEQKFPNGMGHVADHLHNNSFLFGMYSSAGEYTCAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPEISYHRYKAMSDALNKTGRPVFYSLCNWGQDLTFYWGSGIANSWRMSGDVTAEFTRPDSRCPCDGDEYDCKYAGFHCSIMNILNKAAPMGQNAGVGGWNDLDNLEVGVGNLTDDEEKAHFSMWAMVKSPLIIGANVNNLKASSYSIYSQASVIAINQDSNGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALLNGGSVSRPMNTTLEEIFFDSNLGSKKLTSTWDIYDLWANRVDNSTASAILGRNKTATGILYNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPS 470
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
   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  (0, 0)

(no "SCOP Domain" information available for 3LRK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LRK)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (MEL1_YEASX | P04824)
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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BTB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3lrk)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3lrk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MEL1_YEASX | P04824
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.22
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    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
  MEL1_YEASX | P04824
    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
        MEL1_YEASX | P04824: 3lrl 3lrm

(-) Related Entries Specified in the PDB File

3lrl 3lrm