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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL TYW1
 
Authors :  Y. Suzuki, R. Ishitani, O. Nureki
Date :  28 May 07  (Deposition) - 23 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Suzuki, A. Noma, T. Suzuki, M. Senda, T. Senda, R. Ishitani, O. Nureki
Crystal Structure Of The Radical Sam Enzyme Catalyzing Tricyclic Modified Base Formation In Trna
J. Mol. Biol. V. 372 1204 2007
PubMed-ID: 17727881  |  Reference-DOI: 10.1016/J.JMB.2007.07.024
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0026 PROTEIN MJ0257
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: C41(DE3)CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Z2U)

(-) Sites  (0, 0)

(no "Site" information available for 2Z2U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z2U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z2U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z2U)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2Z2U)

(-) 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:279
 aligned with TYW1_METJA | Q57705 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
           TYW1_METJA     1 MIPEEIYKILRKQRYQIDGHTAVKLCGWVRKKMLEDKNCYKSKFYGIETHRCIQCTPSVIWCQQNCIFCWRVLPRDIGIDISQIKEPKWEEPEVVYEKILAMHKRIIMGYAGVLDRVGEKKFKEALEPKHVAISLSGEPTLYPYLDELIKIFHKNGFTTFVVSNGILTDVIEKIEPTQLYISLDAYDLDSYRRICGGKKEYWESILNTLDILKEKKRTCIRTTLIRGYNDDILKFVELYERADVHFIELKSYMHVGYSQKRLKKEDMLQHDEILKLAKMLDENSSYKLIDDSEDSRVALLQNENRKINPKL 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eee..eeee...hhhhhhh....hhhhhhhh.hhh.eeeee.........----------------.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhh.hhhhhhhhhhhh..eeeeee...hhhhhhhh...eeeee.........----..hhhhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhh..eeeeee..------------...hhhhhhhhhhhhhh...eeeeeee....eeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z2u A   1 MIPEEIYKILRKQRYQIDGHTAVKLCGWVRKKMLEDKNCYKSKFYGIETHRCIQCTPSVIWCQQN----------------SQIKEPKWEEPEVVYEKILAMHKRIIMGYAGVLDRVGEKKFKEALEPKHVAISLSGEPTLYPYLDELIKIFHKNGFTTFVVSNGILTDVIEKIEPTQLYISLDAYDLDSY----GGKKEYWESILNTLDILKEKKRTCIRTTLIRGYNDDILKFVELYERADVHFIELKSYM------------DMLQHDEILKLAKMLDENSSYKLIDDSEDSRVALLQNENRKINPKL 311
                                    10        20        30        40        50        60    |    -         - |      90       100       110       120       130       140       150       160       170       180       190|    | 200       210       220       230       240       250  |      -     | 270       280       290       300       310 
                                                                                           65               82                                                                                                          191  196                                                      253          266
   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 2Z2U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Z2U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Z2U)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TYW1_METJA | Q57705)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016833    oxo-acid-lyase activity    Catalysis of the cleavage of a C-C bond by other means than by hydrolysis or oxidation, of a 3-hydroxy acid.
biological process
    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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