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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BDELLOVIBRIO BACTERIOVORUS NUCLEOSIDE DIPHOSPHATE SUGAR HYDROLASE
 
Authors :  S. B. Gabelli, A. H. De La Pena, A. Suarez, L. M. Amzel
Date :  25 Jun 15  (Deposition) - 20 Jan 16  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1GLC2Ligand/IonALPHA-D-GLUCOSE
2GOL4Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4SO46Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:64 , ALA A:76 , GLY A:77 , LYS A:78 , GOL A:204 , HOH A:301 , HOH A:352 , HOH A:359binding site for residue GLC A 201
02AC2SOFTWAREARG A:64 , HOH A:307 , HOH A:325 , HOH A:357 , ARG B:37 , HOH B:358binding site for residue SO4 A 202
03AC3SOFTWAREARG A:12 , ARG A:127 , HOH A:403binding site for residue SO4 A 203
04AC4SOFTWARELYS A:78 , GLU A:119 , LYS A:165 , GLC A:201 , HOH A:363 , HOH B:376binding site for residue GOL A 204
05AC5SOFTWARELEU A:51 , ARG A:127 , ASP A:128 , HOH A:308 , HOH A:309 , HOH A:365 , HOH A:422binding site for residue GOL A 205
06AC6SOFTWAREGLN A:24 , THR A:36 , PHE A:176 , LEU A:177 , ASN A:182 , HOH A:400 , HOH A:443 , ARG B:18binding site for residue PEG A 206
07AC7SOFTWAREARG A:18 , TYR A:19 , HOH A:306 , TYR B:35 , THR B:36 , HOH B:319 , HOH B:354binding site for residue SO4 A 207
08AC8SOFTWAREARG A:37 , HOH A:313 , HOH A:322 , HOH A:342 , HOH A:353 , HOH A:364 , TYR B:63 , ARG B:64 , GLC B:202 , HOH B:338binding site for residue SO4 A 208
09AC9SOFTWARETYR A:35 , THR A:36 , GLY A:179 , HOH A:303 , ARG B:18 , TYR B:19binding site for residue SO4 B 201
10AD1SOFTWARESO4 A:208 , HOH A:322 , ARG B:64 , ALA B:76 , GLY B:77 , LYS B:78 , GOL B:204 , HOH B:302 , HOH B:324 , HOH B:341binding site for residue GLC B 202
11AD2SOFTWAREARG B:127binding site for residue SO4 B 203
12AD3SOFTWAREHOH A:401 , HIS B:42 , ALA B:45 , LYS B:78 , GLU B:119 , LYS B:165 , GLC B:202 , HOH B:400binding site for residue GOL B 204
13AD4SOFTWARELYS B:69 , VAL B:70 , PHE B:71 , GLY B:159 , LYS B:160 , VAL B:161 , SER B:162 , HOH B:327binding site for residue GOL B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C8L)

(-) Exons   (0, 0)

(no "Exon" information available for 5C8L)

(-) 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....eeeeee......eeeeeeee....eeeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee...........eeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8l 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....eeeeeee.....eeeeeee......eeee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee..........eeeeeeeeeee..........eeeeeehhhhhhhhhhh....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c8l 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)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5C8L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C8L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C8L)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  5c8l
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 Related Entries

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

UniProtKB/TrEMBL
        Q6MIH8_BDEBA | Q6MIH8: 5c7q 5c7t

(-) Related Entries Specified in the PDB File

5c7q 5C7Q CONTAINS THE SAME PROTEIN WITHOUT GLUCOSE BOUND
5c7t 5C7T CONTAINS THE SAME PROTEIN