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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-GALACTOSIDASE (EC 3.2.1.22) (MELIBIASE) (TM1192) FROM THERMOTOGA MARITIMA AT 2.34 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  09 Jun 05  (Deposition) - 12 Jul 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Tm1192, Alpha-Galactosidase (Ec 3. 2. 1. 22) (Melibiase), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Alpha-Galactosidase (Ec 3. 2. 1. 22) (Melibiase) (Tm1192) From Thermotoga Maritima At 2. 34 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-GALACTOSIDASE
    Chains: A
    EC Number: 3.2.1.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1192
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:3 , LYS A:6 , THR A:7 , PHE A:8 , ARG A:9 , PHE A:13 , PHE A:24BINDING SITE FOR RESIDUE EDO A 553
2AC2SOFTWARETRP A:65 , PRO A:386 , ASP A:387 , GLY A:400 , ALA A:401 , PRO A:402BINDING SITE FOR RESIDUE EDO A 554
3AC3SOFTWARETRP A:65 , GLY A:400BINDING SITE FOR RESIDUE EDO A 555
4AC4SOFTWAREASN A:290 , TRP A:291 , HOH A:597 , HOH A:692BINDING SITE FOR RESIDUE EDO A 556
5AC5SOFTWARETRP A:190 , TYR A:191 , ASP A:220 , TRP A:257 , LYS A:325 , ASP A:327 , ARG A:383 , ASP A:387BINDING SITE FOR RESIDUE GOL A 557

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZY9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZY9)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZY9)

(-) 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:526
 aligned with AGAL_THEMA | G4FEF4 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:526
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519      
           AGAL_THEMA     - -MEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPGRLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYHYFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMAKVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKKIYALDLSKDEVLNWLFDLFSSLRKMGYRYFKIDFLFAGAVPGERKKNITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPDTAPFWGEHIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKELYSYTCGVLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSEDLRYEIVSSGTLSGNVKIVVDLNSREYHLEKE 525
               SCOP domains -d1zy9a1 A:1-177 Alpha-galactosidase GalA N-terminal domain                                                                                                                       d1zy9a2 A:178-525 Alpha-galactosidase GalA catalytic domain                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee...eeeeee...eeeeeeeeee..eeeeeeeeee...eeeeeeee...eeeee.......eeeee.hhh.....hhhhhhhhh.hhhhhh..eeee.eeee..eeeee......eeeeeee..eeeeeee.....eeeeee...eeeee..hhhhhhhhhhhhhhhhh.........eeeehhhhhhhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhh..eeeeee...eee..hhhhhhhhhhh.ee..ee.eeeee..eeeee....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhh........hhhhhhhhhhhhhhhhhh...eeee....hhhhh....eee...................hhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh....eeee........eeeeeeeee..eeeeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zy9 A   0 HmEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPGRLEVLRTKAPEKVLVNNWQSWGPCRVVDAFSFKPPEIDPNWRYTASVVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVEDGELVAYLEYFDVEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGmENNARVPKHTPTGWCSWYHYFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEmAKVIAENGFIPGIWTAPFSVSETSDVFNEHPDWVVKENGEPKmAYRNWNKKIYALDLSKDEVLNWLFDLFSSLRKmGYRYFKIDFLFAGAVPGERKKNITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGmRIGPDTAPFWGEHIEDNGAPAARWALRNAITRYFmHDRFWLNDPDCLILREEKTDLTQKEKELYSYTCGVLDNmIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNImSEDLRYEIVSSGTLSGNVKIVVDLNSREYHLEKE 525
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169   |   179       189       199       209       219       229       239   |   249       259       269       279      |289       299       309       319       329       339       349       359       369       379  |    389       399       409       419       429       439       449      |459       469       479       489 |     499       509       519      
                             |                                                                                                                                                                         173-MSE                                                               243-MSE                                    286-MSE                          319-MSE                                                        382-MSE                            417-MSE                                456-MSE                            491-MSE                              
                             1-MSE
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  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  (0, 0)

(no "CATH Domain" information available for 1ZY9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZY9)

(-) Gene Ontology  (8, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AGAL_THEMA | G4FEF4)
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:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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.

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 Related Entries

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        AGAL_THEMA | G4FEF4: 5m0x 5m12 5m16 5m1i

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