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(-) Description

Title :  CRYSTAL STRUCTURE OF P. HORIKOSHII TYW2 IN COMPLEX WITH ADOMET
 
Authors :  M. Umitsu, H. Nishimasu, R. Ishitani, O. Nureki
Date :  28 Apr 09  (Deposition) - 15 Sep 09  (Release) - 20 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Wybutosine Modification, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Umitsu, H. Nishimasu, A. Noma, T. Suzuki, R. Ishitani, O. Nureki
Structural Basis Of Adomet-Dependent Aminocarboxypropyl Transfer Reaction Catalyzed By Trna-Wybutosine Synthesizing Enzyme, Tyw2
Proc. Natl. Acad. Sci. Usa V. 106 15616 2009
PubMed-ID: 19717466  |  Reference-DOI: 10.1073/PNAS.0905270106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN PH0793
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0793
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: TYW2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:107 , PHE A:108 , SER A:109 , ARG A:116 , MET A:132 , PHE A:133 , GLY A:135 , HIS A:138 , GLU A:155 , LYS A:156 , MET A:182 , ASP A:183 , ASN A:184 , TYR A:200 , PHE A:207 , HOH A:297BINDING SITE FOR RESIDUE SAM A 279

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A25)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:6 -Lys A:7
2Met A:232 -Pro A:233
3Glu A:235 -Pro A:236
4Ala A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A25)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM5_TYW2PS51684 SAM-dependent methyltransferase TRM5/TYW2-type domain profile.TYW2_PYRHO30-277  1A:30-277

(-) Exons   (0, 0)

(no "Exon" information available for 3A25)

(-) 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:264
 aligned with TYW2_PYRHO | O58523 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:273
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275   
           TYW2_PYRHO     6 IKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPLRPELEPYKHRIAEVYAEVLGVKTVLRKGHIHGETRKPDYELLYGSDTVTVHVENGIKYKLDVAKIMFSPANVKERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILMGYVVRTHEFIPKALSIAKDGAIIHYHNTVPEKLMPREPFETFKRITKEYGYDVEKLNELKIKRYAPGVWHVVLDLRVFKS 278
               SCOP domains d3a25a_ A: Hypothetical protein PH0793                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhh.....eee..eeee..hhhhhhhhhhhhhhhhhhhh..eeee..---------...eee....eeeeee..eeeeee......hhhhhhhhhhhhhhh....eeee.......hhhhhhhhh..eeeee..hhhhhhhhhhhhhhh.....eeee..hhhhh.....eeeeee....hhhhhhhhhhhheeeeeeeeeee..hhhhh...hhhhhhhhhhh...eeeeeeeee..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SAM_MT_TRM5_TYW2  PDB: A:30-277 UniProt: 30-277                                                                                                                                                                                                         - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a25 A   6 IKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPLRPELEPYKHRIAEVYAEVLGVKTVLRKG---------DYELLYGSDTVTVHVENGIKYKLDVAKIMFSPANVKERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILMGYVVRTHEFIPKALSIAKDGAIIHYHNTVPEKLMPREPFETFKRITKEYGYDVEKLNELKIKRYAPGVWHVVLDLRVFKS 278
                                    15        25        35        45        55        65   |     -   |    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275   
                                                                                          69        79
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A25)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TYW2_PYRHO | O58523)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016765    transferase activity, transferring alkyl or aryl (other than methyl) groups    Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3a25
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  TYW2_PYRHO | O58523
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 Related Entries

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

UniProtKB/Swiss-Prot
        TYW2_PYRHO | O58523: 3a26 3k6r

(-) Related Entries Specified in the PDB File

3a26 3a27