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(-) Description

Title :  BETA-GLUCURONIDASE WITH AN ACTIVITY-BASED PROBE (N-ALKYL CYCLOPHELLITOL AZIRIDINE) BOUND
 
Authors :  Y. Jin, L. Wu, J. B. Jiang, H. S. Overkleeft, G. J. Davies
Date :  22 Mar 16  (Deposition) - 12 Apr 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Gh79, Beta-Glucuronidase, Activity-Based Probe, Retaining Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wu, J. Jiang, Y. Jin, W. W. Kallemeijn, C. L. Kuo, M. Artola, W. Dai, C. Van Elk, M. Van Eijk, G. A. Van Der Marel, J. D. C. Codee, B. I. Florea, J. M. F. G. Aerts, H. S. Overkleeft, G. J. Davies
Activity-Based Probes For Functional Interrogation Of Retaining Beta-Glucuronidases.
Nat. Chem. Biol. 2017
PubMed-ID: 28581485  |  Reference-DOI: 10.1038/NCHEMBIO.2395

(-) Compounds

Molecule 1 - BETA-GLUCURONIDASE
    Atcc: 51196
    Chains: A
    EC Number: 3.2.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET-28A
    Expression System Vector Type: PLASMID
    Organism Scientific: ACIDOBACTERIUM CAPSULATUM
    Organism Taxid: 33075

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IF61Ligand/Ion(1R,2S,3R,4S,5S,6R)-7-(8-AZIDOOCTYL)-3,4,5-TRIHYDROXY-

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:45 , GLY A:79 , ASN A:80 , ASP A:105 , ASN A:172 , GLU A:173 , TYR A:243 , GLU A:245 , ARG A:264 , GLU A:287 , TYR A:292 , GLN A:293 , GLY A:294 , HIS A:327 , TYR A:334 , HOH A:2056BINDING SITE FOR RESIDUE IF6 A 1476
2AC2SOFTWAREPHE A:237 , PRO A:282 , ARG A:284 , THR A:322 , HOH A:2022 , HOH A:2023 , HOH A:2173 , HOH A:2294BINDING SITE FOR RESIDUE GOL A 1477
3AC3SOFTWAREASN A:59 , THR A:60 , GLN A:61 , PRO A:341 , LEU A:448 , HOH A:2036BINDING SITE FOR RESIDUE GOL A 1478

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G0Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5G0Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5G0Q)

(-) 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    
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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:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......ee.....eeeee.hhhhh.......hhhhhhhhhhhh...eeeeehhhhh.eee........hhhhh.............eeehhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee..hhhhh..........hhhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhh....eeeeeee..........hhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhhhhh....eeee.........eeee...eeeehhhhhhhhhhhhhh.eeeeeeeee.......eeeeeeee....eeeeeee......eeeeee......eeeeeee..........ee.....hhhhh......ee...eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g0q A  18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTETNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGQFVLHMRKASGALLEFA 475
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447      |460       470     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              454|                 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               458
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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  (0, 0)

(no "SCOP Domain" information available for 5G0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G0Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G0Q)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        C1F2K5_ACIC5 | C1F2K5: 5g0m 5l77
UniProtKB/TrEMBL
        C1F2K5_ACIC5 | C1F2K5: 3vny 3vnz 3vo0

(-) Related Entries Specified in the PDB File

5g0m BETA-GLUCURONIDASE WITH AN ACTIVITY-BASED PROBE (N- ACYL CYCLOPHELLITOL AZIRIDINE) BOUND