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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENOMETHIONINE SUBSTITUTED E. COLI BETA-GLUCURONIDASE
 
Authors :  B. D. Wallace, J. Orans, M. R. Redinbo
Date :  05 Oct 09  (Deposition) - 17 Nov 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Alpha/Beta Barrel, Sugar-Binding Domain, Beta-Sandwich Domain, Glycosyl Hydrolase, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. D. Wallace, H. Wang, K. T. Lane, J. E. Scott, J. Orans, J. S. Koo, M. Venkatesh, C. Jobin, L. A. Yeh, S. Mani, M. R. Redinbo
Alleviating Cancer Drug Toxicity By Inhibiting A Bacterial Enzyme.
Science V. 330 831 2010
PubMed-ID: 21051639  |  Reference-DOI: 10.1126/SCIENCE.1191175

(-) Compounds

Molecule 1 - BETA-GLUCURONIDASE
    ChainsA, B
    EC Number3.2.1.31
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainB834
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneB1617, GURA, GUSA, JW1609, UIDA
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
    SynonymGUS, BETA-D-GLUCURONOSIDE GLUCURONOSOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 26)

Asymmetric Unit (1, 26)
No.NameCountTypeFull Name
1MSE26Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 52)
No.NameCountTypeFull Name
1MSE52Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3K4A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K4A)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Val A:47 -Pro A:48
2Ile A:143 -Pro A:144
3Val B:47 -Pro B:48
4Cys B:197 -Asn B:198
5Lys B:372 -Glu B:373

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K4A)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F2_1PS00719 Glycosyl hydrolases family 2 signature 1.BGLR_ECOLI324-349
 
  2A:324-349
B:324-349
2GLYCOSYL_HYDROL_F2_2PS00608 Glycosyl hydrolases family 2 acid/base catalyst.BGLR_ECOLI399-413
 
  2A:399-413
B:399-413
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F2_1PS00719 Glycosyl hydrolases family 2 signature 1.BGLR_ECOLI324-349
 
  4A:324-349
B:324-349
2GLYCOSYL_HYDROL_F2_2PS00608 Glycosyl hydrolases family 2 acid/base catalyst.BGLR_ECOLI399-413
 
  4A:399-413
B:399-413

(-) Exons   (0, 0)

(no "Exon" information available for 3K4A)

(-) 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:597
 aligned with BGLR_ECOLI | P05804 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:605
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        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       478       488       498       508       518       528       538       548       558       568       578       588       598     
           BGLR_ECOLI     - --MLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLGIGFEAGNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGGKQ 603
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee.....eeeee.........hhhhh.....eee...........hhhhhh...eeeeeeeee........eeeeee.....eeeeee...eeeee......ee..hhhhh....eeeeeeeee..........eeeee.....eeeee.............eeeeee....eeeeeeee.........eeeeeee.....eeee........eee......................eeeeeeee....eeeeeeee....eee....eee..ee..eeeeee...........hhhhhhhhhhhhhhhh..eeee..................eeeee............--------.........hhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeee..................eeee.hhhhhh....hhhhhhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhh....eeeeee..............................hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F2_1      -------------------------------------------------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4a A  -1 SHmLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYVGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVmEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGmVITDENGKKKQSYFHDFFNYAGIHRSVmLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLmVHDHALmDWIGANSYRTSHYPYAEEmLDWADEHGIVVIDETAAVGFNLSLGI--------KELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVmWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVmFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSmYTDmWSEEYQCAWLDmYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGmNFGEKPQQGGKQ 603
                              |      8        18        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    |    -   |   378       388       398       408       418       428       438       448       458       468       478       488       498       508       518 |     528   |   538       548       558       568       578       588  |    598     
                              |                                                                                                     105-MSE                                   147-MSE                     175-MSE                                                                                                                                 311-MSE  |                337-MSE                   363      372                                407-MSE                                 447-MSE                                                              516-MSE         532-MSE                                                    591-MSE        
                              1-MSE                                                                                                                                                                                                                                                                                                                      318-MSE                                                                                                                                                                                                   520-MSE                                                                               

Chain B from PDB  Type:PROTEIN  Length:597
 aligned with BGLR_ECOLI | P05804 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:605
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                              |      8        18        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       478       488       498       508       518       528       538       548       558       568       578       588       598     
           BGLR_ECOLI     - --MLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVMEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGMVITDENGKKKQSYFHDFFNYAGIHRSVMLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLMVHDHALMDWIGANSYRTSHYPYAEEMLDWADEHGIVVIDETAAVGFNLSLGIGFEAGNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVMWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVMFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSMYTDMWSEEYQCAWLDMYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGMNFGEKPQQGGKQ 603
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Glyco_hydro_2_N-3k4aB01 B:9-180                                                                                                                                             -Glyco_hydro_2-3k4aB05 B:182-272                                                            -Glyco_hydro_2_C-3k4aB03 B:274-593                                                                                                                                                                                                                                                                                               ---------- Pfam domains (1)
           Pfam domains (2) ----------Glyco_hydro_2_N-3k4aB02 B:9-180                                                                                                                                             -Glyco_hydro_2-3k4aB06 B:182-272                                                            -Glyco_hydro_2_C-3k4aB04 B:274-593                                                                                                                                                                                                                                                                                               ---------- Pfam domains (2)
         Sec.struct. author ....................eeeeee..................eee...........hhhhhh...eeeeee...........eeee.......ee..ee..ee..........................eeeeee..........eeeee.....eeeee...............eeee...............................eeeeeeee...ee..........................eeeeeeee.....eeeeeee.....eee..eeee..ee.....ee............hhhhhhhhhhhhhhhh..eee..........hhhhhhhh.eeee.............--------.........hhhhhhhhhhhhhhhhhhhh....eeeee..........hhhhhhhhhhhhhh.......ee.ee.........hhhhhh...ee...........hhhhhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhh....eeeeeeeeee................eee......hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_HYDROL_F2_1      -------------------------------------------------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k4a B  -1 SHmLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYVGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVmEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGmVITDENGKKKQSYFHDFFNYAGIHRSVmLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLmVHDHALmDWIGANSYRTSHYPYAEEmLDWADEHGIVVIDETAAVGFNLSLGI--------KELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVmWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVmFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSmYTDmWSEEYQCAWLDmYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGmNFGEKPQQGGKQ 603
                              |      8        18        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    |    -   |   378       388       398       408       418       428       438       448       458       468       478       488       498       508       518 |     528   |   538       548       558       568       578       588  |    598     
                              1-MSE                                                                                                 105-MSE                                   147-MSE                     175-MSE                                                                                                                                 311-MSE  |                337-MSE                   363      372                                407-MSE                                 447-MSE                                                              516-MSE         532-MSE                                                    591-MSE        
                                                                                                                                                                                                                                                                                                                                                         318-MSE                                                                                                                                                                                                   520-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 3K4A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K4A)

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BGLR_ECOLI | P05804)
molecular function
    GO:0004566    beta-glucuronidase activity    Catalysis of the reaction: a beta-D-glucuronoside + H2O = an alcohol + D-glucuronate.
    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.
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:0019391    glucuronoside catabolic process    The chemical reactions and pathways resulting in the breakdown of glucuronosides, compound composed of a hydroxy compound linked to a glucuronate residue.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.

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    Cys B:197 - Asn B:198   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        BGLR_ECOLI | P058043k46 3k4d 3lpf 3lpg 4jhz 5czk

(-) Related Entries Specified in the PDB File

3k46 CRYSTAL STRUCTURE OF NATIVE, UNBOUND, E. COLI BETA- GLUCURONIDASE
3k4d CRYSTAL STRUCTURE OF E. COLI BETA-GLUCURONIDASE WITH GLUCARO-D-LACTAM INHIBITOR BOUND