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(-) Description

Title :  STRUCTURE OF E. COLI BETA-GLUCURONIDASE BOUND WITH A NOVEL, POTENT INHIBITOR 1-((6,8-DIMETHYL-2-OXO-1,2-DIHYDROQUINOLIN-3-YL)METHYL)-1-(2-HYDROXYETHYL)-3-(4-HYDROXYPHENYL)THIOUREA
 
Authors :  A. R. Roberts, B. R. Wallace, M. R. Redinbo
Date :  31 Jul 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Barrel, Sugar-Binding Domain, Beta-Sandwich Domain, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Wallace, A. B. Roberts, R. M. Pollet, J. D. Ingle, K. A. Biernat, S. J. Pellock, M. K. Venkatesh, L. Guthrie, S. K. O'Neal, S. J. Robinson M. Dollinger, E. Figueroa, S. R. Mcshane, R. D. Cohen, J. Jin, S. V. Frye W. C. Zamboni, C. Pepe-Ranney, S. Mani, L. Kelly, M. R. Redinbo
Structure And Inhibition Of Microbiome Beta-Glucuronidases Essential To The Alleviation Of Cancer Drug Toxicity.
Chem. Biol. V. 22 1238 2015
PubMed-ID: 26364932  |  Reference-DOI: 10.1016/J.CHEMBIOL.2015.08.005

(-) Compounds

Molecule 1 - BETA-GLUCURONIDASE
    Chains: A, B
    EC Number: 3.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UIDA, GURA, GUSA, B1617, JW1609
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: GUS,BETA-D-GLUCURONOSIDE GLUCURONOSOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric/Biological Unit (2, 28)
No.NameCountTypeFull Name
157Z2Ligand/Ion1-[(6,8-DIMETHYL-2-OXO-1,2-DIHYDROQUINOLIN-3-YL)METHYL]-1-(2-HYDROXYETHYL)-3-(4-HYDROXYPHENYL)THIOUREA
2MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:361 , GLY A:362 , GLU A:413 , MSE A:447 , TYR A:469 , TYR A:472 , VAL A:473 , HOH A:834 , HOH A:930 , 57Z B:701binding site for residue 57Z A 701
2AC2SOFTWARE57Z A:701 , LEU B:361 , GLY B:362 , ILE B:363 , GLU B:413 , PHE B:448 , TYR B:469 , TYR B:472 , VAL B:473binding site for residue 57Z B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CZK)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Val A:47 -Pro A:48
2Ile A:143 -Pro A:144
3Asn A:198 -His A:199
4Trp A:549 -Asn A:550
5Gln A:558 -Gly A:559
6Gly A:564 -Gly A:565
7Gln A:599 -Gly A:600
8Val B:47 -Pro B:48
9Ile B:143 -Pro B:144
10His B:199 -Ala B:200
11Trp B:549 -Asn B:550

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CZK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CZK)

(-) Exons   (0, 0)

(no "Exon" information available for 5CZK)

(-) 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:600
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee....eeeeeee........hhhhh.....eeee..........hhhhhh...eeeeeeeee.hhhhh..eeeeee.....eeeeee..eeeeeee.....eeee.hhhh....eeeeeeeee..........eeeee.....eeeee.............eeeeee....eeeeeee..........eeeeeee...eeeeeee.....eeeeee.....ee..............eeeeeeee....eeeeeeee....eeee..eeee..ee..eeeee............hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhh.eeeee..........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee......hhhhhhhhhhhhhhhhhh....eeee...........hhhhh..eeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhh....eeeeee..........hhhhh...............hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5czk A  -1 SHmLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVmEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGmVITDENGKKKQSYFHDFFNYAGIHRSVmLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLmVHDHALmDWIGANSYRTSHYPYAEEmLDWADEHGIVVIDETAAVGFNLSLGIGFNKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVmWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVmFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSmYTDmWSEEYQCAWLDmYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGmNFGEKPQQGG 601
                              |      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      |371       381       391       401     | 411       421       431       441     | 451       461       471       481       491       501       511    |  521       531|      541       551       561       571       581       591       601
                              |                                                                                                     105-MSE                                   147-MSE                     175-MSE                                                                                                                                 311-MSE  |                337-MSE                     365|                                   407-MSE                                 447-MSE                                                              516-MSE         532-MSE                                                    591-MSE      
                              1-MSE                                                                                                                                                                                                                                                                                                                      318-MSE                                         369                                                                                                                                                    520-MSE                                                                             


Chain B from PDB  Type:PROTEIN  Length:601
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee.....eeeee.........hhhhh.....eee...........hhhhhh...eeeeeeeee.hhhhh..eeeeee.....eeeeee..eeeeeee.....eeee.hhhh....eeeeeeeee..........eeeee.....eeeee.............eeeeee....eeeeeeee.........eeeeeee...eeeeeee.....eeeeee.....ee..............eeeeeeee....eeeeeeee....eeee..eeee..ee..eeeee............hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhh.eeeee...........................hhhhhhhhhhhhhhhhhhhh....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeee...........hhhhh..eeee..hhhhhh..hhhhhhhhhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhh....eeeeee........hhhhhhh..............hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5czk B  -1 SHmLRPVETPTREIKKLDGLWAFSLDRENCGIDQRWWESALQESRAIAVPGSFNDQFADADIRNYAGNVWYQREVFIPKGWAGQRIVLRFDAVTHYGKVWVNNQEVmEHQGGYTPFEADVTPYVIAGKSVRITVCVNNELNWQTIPPGmVITDENGKKKQSYFHDFFNYAGIHRSVmLYTTPNTWVDDITVVTHVAQDCNHASVDWQVVANGDVSVELRDADQQVVATGQGTSGTLQVVNPHLWQPGEGYLYELCVTAKSQTECDIYPLRVGIRSVAVKGEQFLINHKPFYFTGFGRHEDADLRGKGFDNVLmVHDHALmDWIGANSYRTSHYPYAEEmLDWADEHGIVVIDETAAVGFNLSLGIGFANKPKELYSEEAVNGETQQAHLQAIKELIARDKNHPSVVmWSIANEPDTRPQGAREYFAPLAEATRKLDPTRPITCVNVmFCDAHTDTISDLFDVLCLNRYYGWYVQSGDLETAEKVLEKELLAWQEKLHQPIIITEYGVDTLAGLHSmYTDmWSEEYQCAWLDmYHRVFDRVSAVVGEQVWNFADFATSQGILRVGGNKKGIFTRDRKPKSAAFLLQKRWTGmNFGEKPQQGG 601
                              |      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      |370       380       390       400      |410       420       430       440      |450       460       470       480       490       500       510     | 520       530 |     540       550       560       570       580       590|      600 
                              1-MSE                                                                                                 105-MSE                                   147-MSE                     175-MSE                                                                                                                                 311-MSE  |                337-MSE                     365||                                   407-MSE                                 447-MSE                                                              516-MSE         532-MSE                                                    591-MSE      
                                                                                                                                                                                                                                                                                                                                                         318-MSE                                         367|                                                                                                                                                    520-MSE                                                                             
                                                                                                                                                                                                                                                                                                                                                                                                          369
   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 5CZK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CZK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CZK)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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    Gln A:558 - Gly A:559   [ RasMol ]  
    Gln A:599 - Gly A:600   [ RasMol ]  
    Gly A:564 - Gly A:565   [ RasMol ]  
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    Trp A:549 - Asn A:550   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        BGLR_ECOLI | P05804: 3k46 3k4a 3k4d 3lpf 3lpg 4jhz

(-) Related Entries Specified in the PDB File

4jkk 4jkl 4jkm