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(-) Description

Title :  CRYSTAL STRUCTURE OF TRMD, A M1G37 TRNA METHYLTRANSFERASE WITH SAM-COMPETITIVE COMPOUNDS
 
Authors :  P. A. Elkins, W. G. Bonnette, J. A. Stuckey
Date :  13 Mar 15  (Deposition) - 16 Mar 16  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Trmd, Sam-Binding, Knot, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Elkins, W. G. Bonnette
Crystal Structure Of Trmd, A M1G37 Trna Methyltransferase With Sam-Competitive Compounds
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.228
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21*(DE3)PGRO7
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
14G11Ligand/IonN-(1-{[(3-METHYLBENZOYL)AMINO]METHYL}CYCLOPENTYL)-2,1-BENZOXAZOLE-4-CARBOXAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
14G12Ligand/IonN-(1-{[(3-METHYLBENZOYL)AMINO]METHYL}CYCLOPENTYL)-2,1-BENZOXAZOLE-4-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:87 , SER A:88 , PRO A:89 , GLY A:113 , TYR A:115 , TRP A:131 , SER A:132 , ILE A:133 , GLY A:134 , TYR A:136 , VAL A:137 , LEU A:138 , GLY A:140 , PRO A:144 , GLY A:174 , LEU A:175 , ASP A:177 , HOH A:407binding site for residue 4G1 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YQ3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:160 -Gly A:161
2Arg A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YQ3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YQ3)

(-) Exons   (0, 0)

(no "Exon" information available for 4YQ3)

(-) 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    
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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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeeee......hhhhhhhh..eeee........hhhhhhhhhhhhhh....................ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yq3 A  -7 GLVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN 245
                                     2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       173       183       193       203       213       223       233       243  
                                                                                                                                                                                                  161|                                                                        
                                                                                                                                                                                                   173
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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  (0, 0)

(no "SCOP Domain" information available for 4YQ3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YQ3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YQ3)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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  4yq3
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  TRMD_HAEIN | P43912
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  2.1.1.228
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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 4yq4 4yq5 4yq6 4yq7 4yq8 4yq9 4yqa 4yqb 4yqc 4yqd 4yqg 4yqi 4yqj 4yqk 4yql 4yqn 4yqo 4yqp 4yqq 4yqr 4yqs 4yqt 4yvg 4yvh 4yvi 4yvj 4yvk 5d9f

(-) Related Entries Specified in the PDB File

4ypw 4ypx 4ypy 4ypz 4yq0 4yq1 4yq2 4yq4 4yq5 4yq6 4yq7 4yq8 4yq9 4yqa 4yqb 4yqc 4yqd 4yqg 4yqi 4yqj 4yqk 4yql 4yqn 4yqo 4yqp 4yqq 4yqr 4yqs 4yqt