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(-) Description

Title :  CRYSTAL STRUCTURE OF H. INFLUENZAE TRMD IN COMPLEX WITH SINEFUNGIN AND TRNA
 
Authors :  K. Yoshida, T. Ito, S. Yokoyama
Date :  20 Mar 15  (Deposition) - 15 Jul 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Mtase, Spout, Trna, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Ito, I. Masuda, K. Yoshida, S. Goto-Ito, S. Sekine, S. W. Suh, Y. M. Hou, S. Yokoyama
Structural Basis For Methyl-Donor-Dependent And Sequence-Specific Binding To Trna Substrates By Knotted Methyltransferase Trmd.
Proc. Natl. Acad. Sci. Usa V. 112 E4197 2015
PubMed-ID: 26183229  |  Reference-DOI: 10.1073/PNAS.1422981112

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.228
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TRMD, HI_0202
    Organism Scientific: HAEMOPHILUS INFLUENZAE (STRAIN ATCC 51907 / DSM 11121 / KW20 / RD)
    Organism Taxid: 71421
    Strain: ATCC 51907 / DSM 11121 / KW20 / RD
    Synonym: M1G-METHYLTRANSFERASE,TRNA [GM37] METHYLTRANSFERASE
 
Molecule 2 - TRNA
    Chains: C
    Engineered: YES
    Organism Scientific: THERMOTOGA MARITIMA MSB8
    Organism Taxid: 243274
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SFG2Ligand/IonSINEFUNGIN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:86 , LEU A:87 , SER A:88 , PRO A:89 , GLN A:90 , GLY A:113 , TYR A:115 , GLU A:116 , SER A:132 , ILE A:133 , GLY A:134 , TYR A:136 , LEU A:138 , THR A:139 , GLY A:140 , GLY A:141 , PRO A:144 , ASP B:169 , SER B:170 , ASP B:177 , G C:37binding site for residue SFG A 301
2AC2SOFTWARESER A:170 , ASP A:177 , TYR B:86 , LEU B:87 , SER B:88 , PRO B:89 , GLN B:90 , GLY B:113 , TYR B:115 , GLU B:116 , TRP B:131 , SER B:132 , ILE B:133 , GLY B:134 , TYR B:136 , LEU B:138 , THR B:139 , GLY B:140 , GLY B:141 , PRO B:144binding site for residue SFG B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YVI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:183 -Pro A:184
2Arg B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YVI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YVI)

(-) Exons   (0, 0)

(no "Exon" information available for 4YVI)

(-) 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:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhh.....eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh.......................ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yvi A   0 HMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS 246
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159||     177       187       197       207       217       227       237         
                                                                                                                                                                                          160|                                                                             
                                                                                                                                                                                           169                                                                             


Chain B from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhh........ee.........eehhhhhhhhhhhhhhhhh..eeeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh.......hhhhhhh.................ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yvi B  -2 GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS 246
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         


Chain C from PDB  Type:RNA  Length:71
                                                                                                       
                 4yvi C   1 UGGGAGGUCGUCUAACGGUAGGACGGCGGACUCUGGAUCCGCUGGUGGAGGUUCGAGUCCUCCCCUCCCAG  73
                                    10     || 21        31        41    ||  52        62        72 
                                          16|                          46|                         
                                           18                           48
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YVI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YVI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YVI)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  TRMD_HAEIN | P43912
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRMD_HAEIN | P43912: 1uaj 1uak 1ual 1uam 3axz 4mcb 4mcc 4mcd 4ypw 4ypx 4ypy 4ypz 4yq0 4yq1 4yq2 4yq3 4yq4 4yq5 4yq6 4yq7 4yq8 4yq9 4yqa 4yqb 4yqc 4yqd 4yqg 4yqi 4yqj 4yqk 4yql 4yqn 4yqo 4yqp 4yqq 4yqr 4yqs 4yqt 4yvg 4yvh 4yvj 4yvk 5d9f

(-) Related Entries Specified in the PDB File

4yvg 4yvh 4yvj 4yvk