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(-) Description

Title :  CRYSTAL STRUCTURE OF M. JANNASCHII 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 :  2.00
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 MJ1557
    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: MJ1557
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    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:78 , SER A:80 , ASN A:83 , ARG A:87 , MET A:103 , PHE A:104 , GLY A:106 , TYR A:109 , GLU A:127 , LYS A:128 , ASN A:129 , ALA A:153 , ASP A:154 , ASN A:155 , TYR A:171 , PHE A:178 , HOH A:256 , HOH A:279 , HOH A:304BINDING SITE FOR RESIDUE SAM A 250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A27)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A27)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A27)

(-) 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_METJA5-248  1A:5-248

(-) Exons   (0, 0)

(no "Exon" information available for 3A27)

(-) 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:219
 aligned with TYW2_METJA | Q58952 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
           TYW2_METJA     4 KYQKIGDVVIVKKELSEDEIREIVKRTKCKAILLYTTQITGEFRTPHVKILYGKETETIHKEYGCLFKLDVAKIMWSQGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELKDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHETVAEKIMYERPIERLKFYAEKNGYKLIDYEVRKIKKYAPGVWHVVVDAKFERI 249
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeee-----------------...eeee.----------..eeee....eeeeee..eeeeee......hhhhhhhhhhhhh......eeee.......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhh.....eeeeee....hhhhhhhhhhhheeeeeeeeeeeeee.hhh.hhhhhhhhhhhhhh.eeeeeeeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -SAM_MT_TRM5_TYW2  PDB: A:5-248 UniProt: 5-248                                                                                                                                                                                                       - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a27 A   4 KYQKIGDVVIV-----------------CKAILLYT----------HVKILYGKETETIHKEYGCLFKLDVAKIMWSQGNIEERKRMAFISNENEVVVDMFAGIGYFTIPLAKYSKPKLVYAIEKNPTAYHYLCENIKLNKLNNVIPILADNRDVELKDVADRVIMGYVHKTHKFLDKTFEFLKDRGVIHYHETVAEKIMYERPIERLKFYAEKNGYKLIDYEVRKIKKYAPGVWHVVVDAKFERI 249
                                    13|        -        33     |   -      | 53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      
                                     14                32     39         50
   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 3A27)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A27)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A27)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TYW2_METJA | Q58952)
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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  3a27
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  TYW2_METJA | Q58952
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 Related Entries

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(-) Related Entries Specified in the PDB File

3a25 3a26