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(-) Description

Title :  A GLYCOSIDE HYDROLASE MUTANT WITH AN UNREACTED ACTIVITY BASED PROBE BOUND
 
Authors :  Y. Jin, L. Wu, J. B. Jiang, H. S. Overkleeft, G. J. Davies
Date :  02 Jun 16  (Deposition) - 31 May 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.24
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (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
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-28A
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector Type: PLASMID
    Gene: ACP_2665
    Mutation: YES
    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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3GUX1Ligand/Ion(1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(AZANYLIDENE-{4}-AZANYLIDENE)AMINO]OCTYL]-3,4,5-TRIS(OXIDANYL)-7-AZABICYCLO[4.1.0]HEPTANE-2-CARBOXYLICACID
4PO45Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:33 , THR A:34 , HOH A:626 , HOH A:775binding site for residue PO4 A 501
2AC2SOFTWARETRP A:333 , HOH A:609 , HOH A:668 , HOH A:862binding site for residue PO4 A 502
3AC3SOFTWAREASN A:148 , HOH A:601 , HOH A:708 , HOH A:774 , HOH A:893binding site for residue PO4 A 503
4AC4SOFTWAREARG A:420 , GLU A:422 , HIS A:463 , MET A:464 , ARG A:465binding site for residue PO4 A 504
5AC5SOFTWAREGLY A:103 , LYS A:106 , GLY A:330 , TYR A:331 , GLY A:332 , HOH A:605 , HOH A:640 , HOH A:718 , HOH A:953binding site for residue PO4 A 505
6AC6SOFTWAREGLU A:45 , GLY A:79 , ASN A:80 , PRO A:104 , ASP A:105 , ASN A:172 , GLU A:173 , LEU A:176 , TYR A:243 , GLN A:287 , TYR A:292 , GLN A:293 , GLY A:294 , HIS A:327 , TYR A:334 , HOH A:664binding site for residue GUX A 506
7AC7SOFTWAREHIS A:33 , LYS A:273binding site for residue CL A 507
8AC8SOFTWAREHIS A:108 , HIS A:109 , HOH A:621 , HOH A:839binding site for residue GOL A 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L77)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:214 -Pro A:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L77)

(-) Exons   (0, 0)

(no "Exon" information available for 5L77)

(-) 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:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeee.....eeeee.hhhhh.......hhhhhhhhhhhh...eeeeehhhhh.eee........hhhhh.............eeehhhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhh....eeeeeee..........hhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhhhhh....eeeee........eeee...eeeehhhhhhhhhhhhhh.eeeeeeeee.......eeeeeeee....eeeeeee......eeeeee......eeeeeee..........ee.....hhhhh......ee..ee..eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l77 A  18 SPVRVGLSVDASALGHTIPPDYTGLSYEQAQMANPNYFSGANTQLAGFLRTLGRQGVLRIGGNTSEYTFWNRHAKPTAADEHLAAGPDKGHHAAAREVITPEAVNNLSEFLDKTGWKLIYGLNLGKGTPENAADEAAYVMETIGADRLLAFQLGNEPDLFYRNGIRPASYDFAAYAGDWQRFFTAIRKRVPNAPFAGPDTAYNTKWLVPFADKFKHDVKFISSHYYAEGPPTDPSMTIERLMKPNPRLLGETAGLKQVEADTGLPFRLTQTNSCYQGGKQGVSDTFAAALWAGDLMYQQAAAGSTGINFHGGGYGWYTPVAGTPEDGFIARPEYYGMLLFAQAGAGQLLGAKLTDNSAAPLLTAYALRGTDGRTRIALFNKNLDADVEVAISGVASPSGTVLRLEAPRADDTTDVTFGGAPVGASGSWSPLVQEYVPGHSGQFVLHMRKASGALLEFA 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       457       467
   Legend:   → Mismatch (orange background)
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    → 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 5L77)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L77)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L77)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:214 - Pro A:215   [ RasMol ]  
 

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  5l77
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 Related Entries

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

UniProtKB/Swiss-Prot
        C1F2K5_ACIC5 | C1F2K5: 5g0m 5g0q
UniProtKB/TrEMBL
        C1F2K5_ACIC5 | C1F2K5: 3vny 3vnz 3vo0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L77)