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(-) Description

Title :  STRUCTURE OF ALFA-GALACTOSIDASE (MEL1) FROM SACCHAROMYCES CEREVISIAE WITH MELIBIOSE
 
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 :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Alpha-Galactosidase, Tetramer, Gh27, Melibiose, 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, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1GLA1Ligand/IonALPHA D-GALACTOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3NA1Ligand/IonSODIUM ION
4NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 40)
No.NameCountTypeFull Name
1GLA4Ligand/IonALPHA D-GALACTOSE
2GLC4Ligand/IonALPHA-D-GLUCOSE
3NA-1Ligand/IonSODIUM ION
4NAG32Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:82 , ASN A:105 , GLU A:133 , HOH A:554 , HOH A:691 , HOH A:848BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWAREASN A:175 , GLY A:178 , HOH A:613 , HOH A:825BINDING SITE FOR RESIDUE NAG A 2001
03AC3SOFTWAREGLY A:269 , ASN A:270 , ASN A:381 , LEU A:382 , HOH A:576 , HOH A:585 , HOH A:614 , HOH A:626 , NAG A:3002BINDING SITE FOR RESIDUE NAG A 3001
04AC4SOFTWAREASN A:298 , HOH A:614 , HOH A:626 , HOH A:764 , NAG A:3001BINDING SITE FOR RESIDUE NAG A 3002
05AC5SOFTWAREASP A:273 , SER A:302 , ASN A:403 , HOH A:573 , HOH A:575 , HOH A:662 , HOH A:663 , HOH A:707 , HOH A:798BINDING SITE FOR RESIDUE NAG A 4001
06AC6SOFTWAREASP A:63 , THR A:417 , ASN A:422 , GLU A:425 , HOH A:681 , NAG A:5002BINDING SITE FOR RESIDUE NAG A 5001
07AC7SOFTWARESER A:107 , THR A:424 , HOH A:777 , NAG A:5001BINDING SITE FOR RESIDUE NAG A 5002
08AC8SOFTWARETRP A:328 , TYR A:330 , ILE A:343 , ASN A:370BINDING SITE FOR RESIDUE NAG A 6001
09AC9SOFTWAREHIS A:98 , HIS A:102BINDING SITE FOR RESIDUE NA A 8001
10BC1SOFTWARECYS A:121 , ASP A:209 , GLY A:234 , GLN A:251 , GLA A:481 , HOH A:820 , HOH A:852 , HOH A:871 , HOH A:873BINDING SITE FOR RESIDUE GLC A 480
11BC2SOFTWAREASP A:73 , TYR A:113 , CYS A:121 , LYS A:147 , ASP A:149 , CYS A:186 , TRP A:188 , ARG A:205 , ASP A:209 , GLC A:480BINDING SITE FOR RESIDUE GLA A 481

(-) 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 3LRL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 3LRL)

(-) 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-3lrlA01 A:19-363                                                                                                                                                                                                                                                                                                                               ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeehhhhhh...hhhhhhhhhhhhhhh.hhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhh..eee................................hhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee........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
                 3lrl 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 3LRL)

(-) CATH Domains  (0, 0)

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

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MEL1_YEASX | P04824: 3lrk 3lrm

(-) Related Entries Specified in the PDB File

3lrk 3lrm