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(-) Description

Title :  CRYSTAL STRUCTURE OF TPA1P FROM SACCHAROMYCES CEREVISIAE, TERMINATION AND POLYADENYLATION PROTEIN 1, IN COMPLEX WITH PYRIDINE-2,4-DICARBOXYLIC ACID (2,4-PDCA)
 
Authors :  J. S. Scotti, M. A. Mcdonough, C. J. Schofield
Date :  05 Nov 13  (Deposition) - 19 Nov 14  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  2-Oxoglutarate Oxygenase, Oxygen Sensing, Protein Synthesis Regulation, Double-Stranded Beta Helix, Jellyroll Fold, Prolyl Hydroxylase, Translation, Ribosome, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Horita, J. S. Scotti, C. Thinnes, Y. S. Mottaghi-Taromsari, A. Thalhammer, W. Ge, W. Aik, C. Loenarz, C. J. Schofield, M. A. Mcdonough
Structure Of The Ribosomal Oxygenase Ogfod1 Provides Insights Into The Regio- And Stereoselectivity Of Prolyl Hydroxylases.
Structure V. 23 639 2015
PubMed-ID: 25728928  |  Reference-DOI: 10.1016/J.STR.2015.01.014

(-) Compounds

Molecule 1 - PKHD-TYPE HYDROXYLASE TPA1
    Chains: A
    EC Number: 1.14.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 21-644
    Gene: TPA1, YER049W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: TERMINATION AND POLYADENYLATION PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MN1Ligand/IonMANGANESE (II) ION
3PD21Ligand/IonPYRIDINE-2,4-DICARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , ASP A:161 , HIS A:227 , PD2 A:702 , HOH A:801BINDING SITE FOR RESIDUE MN A 701
2AC2SOFTWARELEU A:156 , HIS A:159 , ASP A:161 , ILE A:171 , HIS A:227 , VAL A:229 , SER A:240 , GLN A:242 , TRP A:244 , MN A:701 , GOL A:703 , GOL A:704 , HOH A:801 , HOH A:812 , HOH A:857 , HOH A:922 , HOH A:993 , HOH A:1158BINDING SITE FOR RESIDUE PD2 A 702
3AC3SOFTWARETYR A:88 , GLN A:92 , ASN A:148 , PD2 A:702 , HOH A:812BINDING SITE FOR RESIDUE GOL A 703
4AC4SOFTWAREHIS A:159 , ASP A:161 , ARG A:166 , PD2 A:702 , HOH A:975 , HOH A:993BINDING SITE FOR RESIDUE GOL A 704
5AC5SOFTWARETYR A:422 , ARG A:423 , ASN A:424 , HOH A:839 , HOH A:1004BINDING SITE FOR RESIDUE GOL A 705
6AC6SOFTWAREPHE A:519 , ASN A:520 , LEU A:523 , LYS A:524 , ILE A:529 , ILE A:530 , ASP A:531 , ASP A:631BINDING SITE FOR RESIDUE GOL A 706

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:494 -A:635

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:51 -Pro A:52
2Phe A:284 -Pro A:285
3Ala A:401 -Pro A:402
4Ile A:407 -Pro A:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NHK)

(-) 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:546
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh..eeee...eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeee......eeeeeeee........hhhhh..eee..eee..ee.....eee.....eeeeee.......eee........eeeeeeeee....hhhhh....hhhhh......ee.hhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhheeeee...hhhhhhhhhhhhhhhhhhh....hhhhh....ee......ee.eee.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhheee.eeeeeeeee.....ee.......hhhhh........eeeeeeee..............eeee...eeeee...eeeeeeeee....eeee..........eeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4nhk A  23 EDKIKGMFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSGDLANLSGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDMSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDVEEVKVDKHRLSIQGWYHIPQVGEEGYIPGELEDFEFPKDERNILSFHEVKHFEKMLKVKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYMMDSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKMKWDVKSC 635
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      |281       291       301   ||  333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553      |589       599       609       619       629      
                                                                                                                                                                                                                                                                      259|                       305|                                                                                                                                                                                                                                     560|                                                
                                                                                                                                                                                                                                                                       279                        328                                                                                                                                                                                                                                      587
   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 4NHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  TPA1_YEAST | P40032
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 Related Entries

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

UniProtKB/Swiss-Prot
        TPA1_YEAST | P40032: 3kt1 3kt4 3kt7 3mgu 4nhl 4nhm

(-) Related Entries Specified in the PDB File

4nhm 4nhn 4nhx