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(-) Description

Title :  STRUCTURAL INSIGHTS INTO THE MECHANISM OF ESCHERICHIA COLI YMDB
 
Authors :  W. Zhang, C. Wang, Y. Song, C. Shao, X. Zhang, J. Zang
Date :  30 Jun 15  (Deposition) - 04 Nov 15  (Release) - 02 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Deacetylase, Adpr, Oaadpr, Macro Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Zhang, C. Wang, Y. Song, C. Shao, X. Zhang, J. Zang
Structural Insights Into The Mechanism Of Escherichia Coli Ymdb: A 2'-O-Acetyl-Adp-Ribose Deacetylase
J. Struct. Biol. V. 192 478 2015
PubMed-ID: 26481419  |  Reference-DOI: 10.1016/J.JSB.2015.10.010

(-) Compounds

Molecule 1 - O-ACETYL-ADP-RIBOSE DEACETYLASE
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YMDB
    Organism Scientific: ESCHERICHIA COLI K12
    Organism Taxid: 83333
    Strain: K12
    Synonym: REGULATOR OF RNASE III ACTIVITY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1APR1Ligand/IonADENOSINE-5-DIPHOSPHORIBOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ASP A:11 , ILE A:12 , ALA A:23 , ASN A:25 , GLY A:30 , GLY A:31 , GLY A:32 , GLY A:33 , VAL A:34 , ASP A:35 , ALA A:120 , SER A:122 , THR A:123 , GLY A:124 , VAL A:125 , TYR A:126 , TYR A:159 , HOH A:504 , HOH A:514 , HOH A:522 , HOH A:528 , HOH A:532 , HOH A:537 , HOH A:541 , HOH A:542 , HOH A:561binding site for residue APR A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CB3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:150 -Pro A:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CB3)

(-) Exons   (0, 0)

(no "Exon" information available for 5CB3)

(-) 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:171
                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.......eeeee..........hhhhhhhhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cb3 A   3 TRIHVVQGDITKLAVDVIVNAANPSLMGGGGVDGAIHRAAGPALLDACLKVRQQQGDCPTGHAVITLAGDLPAKAVVHTVGPVWRGGEQNEDQLLQDAYLNSLRLVAANSYTSVAFPAISTGVYGYPRAAAAEIAVKTVSEFITRHALPEQVYFVCYDEENAHLYERLLTQ 173
                                    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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  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 5CB3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CB3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CB3)

(-) Gene Ontology  (10, 10)

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
        YMDB_ECOLI | P0A8D6: 1spv 5cb5 5cms

(-) Related Entries Specified in the PDB File

5cb5