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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 :  1.77
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  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2FE1Ligand/IonFE (III) ION
3GOL1Ligand/IonGLYCEROL
4LVN1Mod. Amino Acid(3S)-4-OXO-L-VALINE
5SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2FE-1Ligand/IonFE (III) ION
3GOL2Ligand/IonGLYCEROL
4LVN2Mod. Amino Acid(3S)-4-OXO-L-VALINE
5SO48Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:159 , ASP A:161 , HIS A:227 , AKG A:702 , HOH A:1495BINDING SITE FOR RESIDUE FE A 701
2AC2SOFTWARELEU A:156 , HIS A:159 , ASP A:161 , ILE A:171 , TYR A:173 , HIS A:227 , LVN A:229 , ARG A:238 , GLN A:242 , FE A:701 , HOH A:859 , HOH A:1151 , HOH A:1167 , HOH A:1414 , HOH A:1495BINDING SITE FOR RESIDUE AKG A 702
3AC3SOFTWAREALA A:544 , GLY A:545 , TRP A:546 , GLU A:547 , SER A:548 , HOH A:985BINDING SITE FOR RESIDUE SO4 A 703
4AC4SOFTWARELYS A:152 , VAL A:234 , ASP A:235 , HOH A:1444BINDING SITE FOR RESIDUE SO4 A 704
5AC5SOFTWAREARG A:179 , LYS A:180 , LYS A:182 , HOH A:1204BINDING SITE FOR RESIDUE SO4 A 705
6AC6SOFTWARELYS A:180 , LYS A:182 , SER A:183 , HOH A:922 , HOH A:979 , HOH A:1180 , HOH A:1276BINDING SITE FOR RESIDUE SO4 A 706
7AC7SOFTWAREARG A:423 , ASN A:424 , HOH A:1051 , HOH A:1337BINDING SITE FOR RESIDUE GOL A 707

(-) SS Bonds  (1, 1)

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

(-) 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 3KT7)

(-) 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 3KT7)

(-) 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:558
 aligned with TPA1_YEAST | P40032 from UniProtKB/Swiss-Prot  Length:644

    Alignment length:612
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633  
           TPA1_YEAST    24 DKIKGMFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSGDLANLSGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDMSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDVEEVKVDKHRLSIQGWYHIPQVGEEGYIPGEEEAWVRNNTSTLAQIESNVLEDFEFPKDERNILSFHEVKHFEKMLKGDAGAKTDNTPKESMTSVISDSVKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYMMDDDEDNKQYLKEDVEDASVYRADDSGDSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKMKWDVKSC 635
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------       -----------------------------                      -----Ofd1_CTDD-3kt7A01 A:333-635                                                                                                                                                                                                                                                                                     Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh......eee....hhhhhhhhhhhhhhhh..eeee...eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeee......eeeeeeee........hhhhh..eee..eee..ee.....eee.....eeeeee.......eee........eeeeeeeee...........hhhhhhhhhhhh-------hhhhhhh......ee.hhhhhhhhhhhhh----------------------...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhheeee....hhhhhhhhhhhhhhhhhhh....hhhhh....ee......ee.eee.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh......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
                 3kt7 A  24 DKIKGMFNPKIWDKTFQDGLKKEIEDSQPYNWGTIHELVNDDLLRAVRKEIETEIHFTKKETDIYRVNQSGDLANLSGLDWDDLSRLPNLFKLRQILYSKQYRDFFGYVTKAGKLSGSKTDMSINTYTKGCHLLTHDDVIGSRRISFILYLPDPDRKWKSHYGGGLRLFPSILPNVPHSDPSAKLVPQFNQIAFFKVLPGFSFHDvEEVKVDKHRLSIQGWYHIPQVGEEGYIPGEEEAWVRNNTS-------NVLEDFEFPKDERNILSFHEVKHFEKMLK----------------------VKLSEAEFTYLSQYISPEHLSSKGIEKLQKQFVENSSLQIESFLNDDKSELLKKVIKQKELEQECPYHSKDVKAPWKTAIPPHKARYLYIDGKEYRNFQTEADILEALNNNDLPNFQFTKDAIKIISDASGNSRENNFDAELALIDLAVFHKSTIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLKSNPDIIDAVLEGTLCLTPSAGWESGELGGYELYMMD-------------------------DSVLINDPPAWNTFNLVLRDESVLEFVKYVSWSAKSSRWDVKMKWDVKSC 635
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     | 233       243       253       263     |   -   |   283       293       303 |       -         -    |  333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553      |  -         -         -  |    593       603       613       623       633  
                                                                                                                                                                                                                                       229-LVN                                 269     277                         305                    328                                                                                                                                                                                                                                     560                       586                                                 

   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 3KT7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KT7)

(-) 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 3kt4 3mgu 4nhk 4nhl 4nhm

(-) Related Entries Specified in the PDB File

3kt1 3kt4