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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BDELLOVIBRIO BACTERIOVORUS NUCLEOSIDE DIPHOSPHATE SUGAR HYDROLASE IN COMPLEX WITH ADP-RIBOSE
 
Authors :  S. B. Gabelli, A. H. De La Pena, A. Suarez, L. M. Amzel
Date :  24 Jun 15  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nudix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. De La Pena, A. Suarez, K. C. Duong-Ly, A. J. Schoeffield, M. A. Pizarro-Dupuy, M. Zarr, S. A. Pineiro, L. M. Amzel, S. B. Gabelli
Structural And Enzymatic Characterization Of A Nucleoside Diphosphate Sugar Hydrolase From Bdellovibrio Bacteriovorus
Plos One V. 10 41716 2015
PubMed-ID: 26524597  |  Reference-DOI: 10.1371/JOURNAL.PONE.0141716

(-) Compounds

Molecule 1 - NUDF PROTEIN
    Chains: A, B
    EC Number: 3.6.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PET24
    Expression System Taxid: 866768
    Gene: NUDF, BD3179
    Mutation: YES
    Organism Scientific: BDELLOVIBRIO BACTERIOVORUS
    Organism Taxid: 264462
    Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
1APR2Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE
2GOL7Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG01Ligand/Ion2-(2-METHOXYETHOXY)ETHANOL
5PGE1Ligand/IonTRIETHYLENE GLYCOL
6SO46Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:19 , ARG A:64 , GLY A:77 , LYS A:78 , GLU A:119 , GLY A:139 , LYS A:165 , HOH A:309 , HOH A:321 , HOH A:329 , HOH A:330 , HOH A:354 , HOH A:381 , HOH A:389 , THR B:36 , ARG B:37 , GLU B:38 , ILE B:114 , GLY B:115 , SO4 B:201binding site for residue APR A 201
02AC2SOFTWAREARG A:18 , TYR A:19 , HOH A:311 , TYR B:35 , THR B:36 , HOH B:320binding site for residue SO4 A 202
03AC3SOFTWAREARG A:12 , GLN A:26 , ARG A:127 , HOH A:334 , PEG B:202binding site for residue SO4 A 203
04AC4SOFTWARELYS A:90 , HOH A:301 , HOH A:343binding site for residue SO4 A 204
05AC5SOFTWAREILE A:14 , LEU A:51 , ARG A:127 , ASP A:128 , HOH A:346 , HOH A:353 , HOH A:380binding site for residue GOL A 205
06AC6SOFTWARELYS A:69 , VAL A:70 , PHE A:71 , GLY A:159 , LYS A:160 , VAL A:161 , SER A:162 , HOH A:314 , HIS B:111binding site for residue GOL A 206
07AC7SOFTWAREPRO A:149 , ALA A:150 , MET A:153 , ASP A:174 , HOH A:324binding site for residue GOL A 207
08AC8SOFTWAREHIS A:61 , VAL A:70 , HOH A:355binding site for residue PG0 A 208
09AC9SOFTWARETHR A:34 , TYR A:35 , THR A:36 , GLY A:179 , ARG B:18 , TYR B:19binding site for residue SO4 A 209
10AD1SOFTWAREARG A:37 , HOH A:347 , HOH A:349 , HOH A:371 , TYR B:63 , ARG B:64 , APR B:203binding site for residue SO4 A 210
11AD2SOFTWARETYR A:63 , ARG A:64 , APR A:201 , ARG B:37 , GLY B:115 , HOH B:317 , HOH B:331binding site for residue SO4 B 201
12AD3SOFTWAREGLN A:26 , THR A:36 , PHE A:176 , LEU A:177 , ASN A:182 , SO4 A:203 , HOH A:315 , ARG B:18binding site for residue PEG B 202
13AD4SOFTWARETHR A:36 , ARG A:37 , GLU A:38 , ILE A:114 , GLY A:115 , TYR A:116 , SO4 A:210 , HOH A:347 , TYR B:19 , ARG B:64 , ALA B:76 , GLY B:77 , LYS B:78 , GLU B:119 , GLN B:138 , GLY B:139 , GLN B:140 , LYS B:165 , GOL B:204 , HOH B:330 , HOH B:349 , HOH B:353 , HOH B:371binding site for residue APR B 203
14AD5SOFTWARELYS B:78 , ASP B:80 , ARG B:91 , GLU B:92 , APR B:203 , HOH B:338binding site for residue GOL B 204
15AD6SOFTWARELYS B:69 , VAL B:70 , PHE B:71 , LEU B:72 , GLY B:159 , LYS B:160 , SER B:162 , PGE B:208 , HOH B:343binding site for residue GOL B 205
16AD7SOFTWAREARG A:18 , HIS B:131 , HOH B:319 , HOH B:358binding site for residue GOL B 206
17AD8SOFTWAREASN B:56 , GLU B:146 , LYS B:148binding site for residue GOL B 207
18AD9SOFTWAREHIS B:61 , LYS B:160 , GOL B:205 , HOH B:321binding site for residue PGE B 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C7T)

(-) Exons   (0, 0)

(no "Exon" information available for 5C7T)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeeee....eeeeeeee.....eeeeeee....eeeeeee.....eeeeeeeehhhheeeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee...........eeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c7t A   1 MKHLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGQFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEWN 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  


Chain B from PDB  Type:PROTEIN  Length:179
                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee....eeeeeeee.....eeeeeee....eeeeee......eeeeeeee....eeeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee...........eeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c7t B   3 HLEEKTLSTRQIFKGRYLKIEQDQVQAPDGRTYTREYILHPGAAMMIPLLPNGNVVMIHQYRHAVKKVFLEFPAGKRDHNEETLLTAKRELLEETGYEAKDWKFLTTIHPVIGYSNEHIDLYLARDLTHLEQRLDQGQFIEVVEVKPADLMQLVLEGKVSDVKTQIGAFWLDKFLRGEW 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
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  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 5C7T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C7T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C7T)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q6MIH8_BDEBA | Q6MIH8: 5c7q 5c8l

(-) Related Entries Specified in the PDB File

5c7q 5C7Q CONTAINS THE SAME PROTEIN WITHOUT ADPR