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(-) Description

Title :  CRYSTAL STRUCTURE OF A BETA-GALACTOSIDASE FROM BACTEROIDES THETAIOTAOMICRON
 
Authors :  K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  09 May 08  (Deposition) - 27 May 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Crystal Structure, Beta-Galactosidase, Bacteroides Thetaiotaomicron, Protein Structure Initiative Ii, Psi Ii, Nysgxrc, 11092F, Structural Genomics, New York Sgx Research Center For Structural Genomics, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Palani, D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Of A Beta-Galactosidase From Bacteroides Thetaiotaomicron.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-GALACTOSIDASE
    Atcc: 29148
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 24-625
    Gene: BT_0290
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 21)

Asymmetric/Biological Unit (1, 21)
No.NameCountTypeFull Name
1MSE21Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3D3A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D3A)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:117 -Pro A:118
2Phe A:313 -Pro A:314
3Gly A:569 -Pro A:570

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D3A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D3A)

(-) Exons   (0, 0)

(no "Exon" information available for 3D3A)

(-) 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:604
 aligned with Q8AB22_BACTN | Q8AB22 from UniProtKB/TrEMBL  Length:779

    Alignment length:628
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641        
         Q8AB22_BACTN    22 QSSEGTFEVGKNTFLLNGEPFVVKAAEIHYPRIPKEYWEHRIKMCKALGMNTICLYVFWNFHEPEEGRYDFAGQKDIAAFCRLAQENGMYVIVRPGPYVCAEWEMGGLPWWLLKKKDIKLREQDPYYMERVKLFLNEVGKQLADLQISKGGNIIMVQVENEYGAFGIDKPYISEIRDMVKQAGFTGVPLFQCDWNSNFENNALDDLLWTINFGTGANIDEQFKRLKELRPDTPLMCSEFWSGWFDHWGAKHETRSAEELVKGMKEMLDRNISFSLYMTHGGTSFGHWGGANFPNFSPTCTSYDYDAPINESGKVTPKYLEVRNLLGNYLPEGETLPEIPDSIPTIAIPTIKMTEMAVLFDNLPHPKESEDIRTMEAFDQGWGSILYRTSLSASDKEQTLLITEAHDWAQVFLNGKKLATLSRLKGEGVVKLPPLKEGDRLDILVEAMGRMNFGKGIYDWKGITEKVELQSDKGVELVKDWQVYTIPVDYSFARDKQYKQQENAENQPAYYRSTFNLNELGDTFLNMMNWSKGMVWVNGHAIGRYWEIGPQQTLYVPGCWLKKGENEIIILDMAGPSKAETEGLRQPILDVQRGNGAYAHRKMGENLDLTNETPVYQGIFKSGNGWQHV 649
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eee..eee..eeeeehhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh........hhhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh..hhhhhhhhhhhhhhhh.....eeeee...hhhhh.....eeeeeee...hhhhhhhhhhhhh.....eeeeee..............hhhhhhhhhhhhhh...eeeee.............ee....ee.................hhhhhhhhhhhh....................eeeee..eeee.hhhh...eee....hhhhhh....eeeeeeee......eeeeeeeee.eeeeee..eeeeeee......eeee......eeeeeeee......hhhhhh...eeeeeeeeee..eeee...eeeeee..hhhhhhh.....-----...eeeeeeeee.....eeee.....eeeeee..eeeeeee......eeeehhhhh..eeeeeeeee.......eeeee..............hhhhh..-------------------..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3a A  22 SLSEGTFEVGKNTFLLNGEPFVVKAAEIHYPRIPKEYWEHRIKmCKALGmNTICLYVFWNFHEPEEGRYDFAGQKDIAAFCRLAQENGmYVIVRPGPYVCAEWEmGGLPWWLLKKKDIKLREQDPYYmERVKLFLNEVGKQLADLQISKGGNIImVQVENEYGAFGIDKPYISEIRDmVKQAGFTGVPLFQCDWNSNFENNALDDLLWTINFGTGANIDEQFKRLKELRPDTPLmCSEFWSGWFDHWGAKHETRSAEELVKGmKEmLDRNISFSLYmTHGGTSFGHWGGANFPNFSPTCTSYDYDAPINESGKVTPKYLEVRNLLGNYLPEGETLPEIPDSIPTIAIPTIKmTEmAVLFDNLPHPKESEDIRTmEAFDQGWGSILYRTSLSASDKEQTLLITEAHDWAQVFLNGKKLATLSRLKGEGVVKLPPLKEGDRLDILVEAmGRmNFGKGIYDWKGITEKVELQSDKGVELVKDWQVYTIPVDYSFARDKQYKQ-----NQPAYYRSTFNLNELGDTFLNmmNWSKGmVWVNGHAIGRYWEIGPQQTLYVPGCWLKKGENEIIILDmAGPSKAETEGLRQPILDVQRGNGAYAHRKmGE-------------------GHHHH 630
                                    31        41        51        61   |    71        81        91       101       111       121    |  131       141       151       161       171    |  181       191       201       211       221       231       241       251    |  261       271       281  |  | 291      |301       311       321       331       341       351       361       371 |  |  381       391   |   401       411       421       431       441       451       461      |471       481       491       501       511        |-    |  531       541     ||551  |    561       571       581       591 |     601       611       621 | |     -         -   |    
                                                                      65-MSE |                                    110-MSE         126-MSE                149-MSE                    176-MSE                199-MSE                                                  256-MSE                     284-MSE       298-MSE                                                                    373-MSE               395-MSE                                                                  468-MSE                                             520   526                  547-MSE  |                                    593-MSE                       623-MSE               626    
                                                                            71-MSE                                                                                                                                                                                                                 287-MSE                                                                                  376-MSE                                                                                        471-MSE                                                                      548-MSE |                                                                    625                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              554-MSE
   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 3D3A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D3A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D3A)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8AB22_BACTN | Q8AB22)
molecular function
    GO:0004565    beta-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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.
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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  Cis Peptide Bonds
    Gly A:117 - Pro A:118   [ RasMol ]  
    Gly A:569 - Pro A:570   [ RasMol ]  
    Phe A:313 - Pro A:314   [ RasMol ]  
 

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