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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE DXO IN COMPLEX WITH (3'-NADP)+ AND CALCIUM ION
 
Authors :  S. K. Doamekpor, L. Tong
Date :  24 Jan 17  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Nadp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Jiao, S. K. Doamekpor, J. G. Bird, B. E. Nickels, L. Tong, R. P. Hart, M. Kiledjian
5' End Nicotinamide Adenine Dinucleotide Cap In Human Cells Promotes Rna Decay Through Dxo-Mediated Denadding.
Cell V. 168 1015 2017
PubMed-ID: 28283058  |  Reference-DOI: 10.1016/J.CELL.2017.02.019

(-) Compounds

Molecule 1 - DECAPPING AND EXORIBONUCLEASE PROTEIN
    Chains: A
    EC Number: 3.1.13.-, 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)ROSETTA
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DXO, DOM3Z, NG6
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DXO,DOM-3 HOMOLOG Z

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
10WD1Ligand/Ion[[(2R,3S,4R,5R)-5-(3-AMINOCARBONYL-4H-PYRIDIN-1-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHYL HYDROGENPHOSPHATE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:192 , ASP A:236 , GLU A:253 , LEU A:254 , 0WD A:402 , HOH A:501 , HOH A:506 , HOH A:515binding site for residue CA A 401
2AC2SOFTWAREARG A:58 , ARG A:95 , GLU A:97 , TRP A:131 , ARG A:132 , GLY A:133 , HIS A:134 , GLU A:164 , TYR A:189 , GLY A:233 , GLU A:234 , LYS A:255 , GLN A:280 , CA A:401 , HOH A:502 , HOH A:506 , HOH A:513 , HOH A:515 , HOH A:525 , HOH A:535 , HOH A:553 , HOH A:600binding site for residue 0WD A 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:88 -Pro A:89
2Pro A:247 -Pro A:248
3Ala A:369 -Pro A:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ULI)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..hhhhhh.........eeeeeeee.....ee.......ee...........ee........ee.........hhhhhhhhhhhh.......hhhhhheeeehhhhhhhhhhhhh....eeeeeeee..eeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhee............ee...eeeeeeeeee..eeeeeeee..ee............eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeee.hhhhhhh.......hhhhhhhhhhhhhhhhhhhh......eeeeeee.....eeeeeee.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uli A  27 PSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQ 384
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
   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 5ULI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:369 - Pro A:370   [ RasMol ]  
    Pro A:247 - Pro A:248   [ RasMol ]  
    Tyr A:88 - Pro A:89   [ RasMol ]  
 

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  DXO_MOUSE | O70348
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 Related Entries

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

UniProtKB/Swiss-Prot
        DXO_MOUSE | O70348: 3fqi 3fqj 4j7l 4j7m 4j7n

(-) Related Entries Specified in the PDB File

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