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(-) Description

Title :  CRYSTAL STRUCTURE OF TPA1 FROM SACCHAROMYCES CEREVISIAE, A COMPONENT OF THE MESSENGER RIBONUCLEOPROTEIN COMPLEX
 
Authors :  H. S. Kim, H. L. Kim, K. H. Kim, D. J. Kim, S. J. Lee, J. Y. Yoon, H. J. Yoon, H. S. B. Park, S. -J. Kim, J. Y. Lee, S. W. Suh
Date :  24 Nov 09  (Deposition) - 19 Jan 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.73
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tpa1, Double-Stranded Beta Helix Fold, Dioxygenase, Iron, Mrnp Complex, Prolyl Hydroxylase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. S. Kim, H. L. Kim, K. H. Kim, D. J. Kim, S. J. Lee, J. Y. Yoon, H. J. Yoon, H. Y. Lee, S. B. Park, S. -J. Kim, J. Y. Lee, S. W. Suh
Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A Component Of The Messenger Ribonucleoprotein Complex
Nucleic Acids Res. V. 38 2099 2010
PubMed-ID: 20040577  |  Reference-DOI: 10.1093/NAR/GKP1151

(-) Compounds

Molecule 1 - PKHD-TYPE HYDROXYLASE TPA1
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A(+)
    Expression System StrainROSSETA2(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL TRUNCATED FORM (RESIDUES 21-644)
    GeneTPA1, YER049W
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymTERMINATION AND POLYADENYLATION PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1FE1Ligand/IonFE (III) ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , ASP A:161 , HIS A:227 , HOH A:859BINDING SITE FOR RESIDUE FE A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KT4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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 3KT4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.TPA1_YEAST141-247  1A:141-247
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.TPA1_YEAST141-247  2A:141-247

(-) Exons   (0, 0)

(no "Exon" information available for 3KT4)

(-) Sequences/Alignments

Asymmetric 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:563
 aligned with TPA1_YEAST | P40032 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:615
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631     
           TPA1_YEAST    22 EEDKIKGMFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSGDLANLSGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDMSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDVEEVKVDKHRLSIQGWYHIPQVGEEGYIPGEEEAWVRNNTSTLAQIESNVLEDFEFPKDERNILSFHEVKHFEKMLKGDAGAKTDNTPKESMTSVISDSVKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYMMDDDEDNKQYLKEDVEDASVYRADDSGDSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKMKWDVKSCD 636
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------     --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                      -----Ofd1_CTDD-3kt4A01 A:333-636                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeee...eeeee..-----..........hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeee......eeeeeeee........hhhhh..eee..eee..ee.....eee......eeeee.......eee........eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhhhhhhhhhh----------------------...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhhh....hhhhh....ee......ee.eee.........hhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhheee.eeeeeeeee.....ee.......hhhhh....eeeeeeeeeeee..............eeee..-------------------------..eeeee...eeeeeeeee....eeee..........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:141-247 UniProt: 141-247                                                                 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kt4 A  22 EEDKIKGmFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSG-----SGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDmSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDVEEVKVDKHRLSIQGWYHIPQVGEEGYIPGEEEAWVRNNTSTLAQIESNVLEDFEFPKDERNILSFHEVKHFEKmLK----------------------VKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGmDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYmmD-------------------------DSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKmKWDVKSCD 636
                                   |31        41        51        61        71        81        91  |    101       111       121       131       141   |   151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301 | |     -         -      |331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551      |||-         -         -    |  591       601       611       621      |631     
                                  29-MSE                                                           94   100                                          145-MSE                                                                                                                                                       303-MSE                  328                                                                                                                                                                                  509-MSE                                          558-MSE                     586                                       628-MSE    
                                                                                                                                                                                                                                                                                                                     305                                                                                                                                                                                                                                                           559-MSE                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    560                                                                            

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3KT4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KT4)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (TPA1_YEAST | P40032)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035516    oxidative DNA demethylase activity    Catalysis of the removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    GO:0031543    peptidyl-proline dioxygenase activity    Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl hydroxy-L-proline + succinate + CO2.
    GO:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
biological process
    GO:0006307    DNA dealkylation involved in DNA repair    The repair of alkylation damage, e.g. the removal of the alkyl group at the O6-position of guanine by O6-alkylguanine-DNA alkyltransferase (AGT).
    GO:0000288    nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay    A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0035511    oxidative DNA demethylation    Removal of the methyl group from one or more nucleotides within a DNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
    GO:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0018188    peptidyl-proline di-hydroxylation    The modification of peptidyl-proline to form trans-2,3-cis-3,4-dihydroxy-L-proline.
    GO:0006449    regulation of translational termination    Any process that modulates the frequency, rate or extent of translational termination.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TPA1_YEAST | P400323kt1 3kt7 3mgu 4nhk 4nhl 4nhm

(-) Related Entries Specified in the PDB File

3kt1 3kt7