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(-) Description

Title :  THE STRUCTURE OF HUMAN PDE12 RESIDUES 161-609
 
Authors :  R. T. Nolte, B. Wisely, L. Wang, E. R. Wood
Date :  26 Mar 15  (Deposition) - 17 Jun 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Pde12 2'-5'A Eep Nuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Wood, R. Bledsoe, J. Chai, P. Daka, H. Deng, Y. Ding, S. Harris-Gurley, L. H. Kryn, E. Nartey, J. Nichols, R. T. Nolte, N. Prabhu, C. Rise, T. Sheahan, J. B. Shotwell, D. Smith, V. Tai, J. D. Taylor, G. Tomberlin, L. Wang, B. Wisely, S. You, B. Xia, H. Dickso
The Role Of Phosphodiesterase 12 (Pde12) As A Negative Regulator Of The Innate Immune Response And The Discovery O Antiviral Inhibitors.
J. Biol. Chem. V. 290 19681 2015
PubMed-ID: 26055709  |  Reference-DOI: 10.1074/JBC.M115.653113

(-) Compounds

Molecule 1 - 2',5'-PHOSPHODIESTERASE 12
    Chains: A
    EC Number: 3.1.4.-, 3.1.13.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 469008
    Expression System Variant: DE3
    Fragment: UNP RESIDUES 155-609
    Gene: PDE12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 2-PDE,MITOCHONDRIAL DEADENYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:351 , HOH A:809 , HOH A:824 , HOH A:848 , HOH A:1008 , HOH A:1031binding site for residue MG A 701
2AC2SOFTWARESER A:192 , GLY A:253 , ASP A:254 , GLY A:255 , ARG A:257 , PHE A:258 , HOH A:807binding site for residue GOL A 702
3AC3SOFTWAREGLN A:396 , HIS A:397 , ASP A:398 , HOH A:861 , HOH A:876 , HOH A:904binding site for residue GOL A 703
4AC4SOFTWARELEU A:393 , GLN A:396binding site for residue GOL A 704
5AC5SOFTWAREASN A:568 , LYS A:609 , HOH A:803binding site for residue GOL A 705
6AC6SOFTWARETRP A:459 , PRO A:461 , ARG A:467 , ASN A:498 , HOH A:1047binding site for residue GOL A 706
7AC7SOFTWARELYS A:417 , LEU A:534 , THR A:535 , HOH A:922binding site for residue GOL A 707

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z0V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:590 -Pro A:591

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z0V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z0V)

(-) 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:434
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.............eeeee..hhhhheeeeeee.........eee..........hhhhh...eeeeee..........eeee............hhhhhhhhh.......eeeeeeee..hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhh.eeeeeee...eeeeeeee...eeeeee..eehhhhhhhh..hhhhhhhh..hhhhhhhhhhh..eeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhhhh......eeeeee......hhhhhhhhhhee...hhhhhh..........ee....eee........eee..eee..eeeeee...eeeeee....hhhhhhh...............eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0v A 161 PPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAGSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGHSRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQTEFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDSLVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPLHKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWHPKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVINGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCLDYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK 609
                                   170       180       190       200      |225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605    
                                                                        207|                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                         223
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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 4Z0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z0V)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:590 - Pro A:591   [ RasMol ]  
 

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  4z0v
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  PDE12_HUMAN | Q6L8Q7
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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE12_HUMAN | Q6L8Q7: 4z2b 4zkf

(-) Related Entries Specified in the PDB File

4z2b