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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA (UM34/CM34) METHYLTRANSFERASE TRML FROM ESCHERICHIA COLI WITH SAH
 
Authors :  R. J. Liu, M. Zhou, E. D. Wang
Date :  18 Feb 13  (Deposition) - 31 Jul 13  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Spout, Methyltransferase, Trna Modification, Trml, Deep Trefoil Knot, Sam Binding, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Liu, M. Zhou, Z. P. Fang, M. Wang, X. L. Zhou, E. D. Wang
The Trna Recognition Mechanism Of The Minimalist Spout Methyltransferase, Trml
Nucleic Acids Res. V. 41 7828 2013
PubMed-ID: 23804755  |  Reference-DOI: 10.1093/NAR/GKT568

(-) Compounds

Molecule 1 - TRNA (CYTIDINE(34)-2'-O)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.207
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRML, YIBK, B3606, JW3581
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRML

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , LEU A:78 , THR A:79 , PHE A:99 , GLY A:100 , PRO A:101 , GLU A:102 , GLY A:105 , ILE A:120 , ILE A:122 , MET A:124 , SER A:130 , MET A:131 , ASN A:132 , LEU A:133 , EPE A:202 , HOH A:303BINDING SITE FOR RESIDUE SAH A 201
2AC2SOFTWARETHR A:79 , THR A:80 , LYS A:81 , THR A:103 , GLY A:105 , LEU A:106 , SAH A:201BINDING SITE FOR RESIDUE EPE A 202
3AC3SOFTWAREASN A:17 , ARG A:20 , LEU A:21 , MET B:131 , ASN B:132 , ASN B:135 , HOH B:310BINDING SITE FOR RESIDUE EDO B 201
4AC4SOFTWARELEU B:78 , THR B:79 , THR B:80 , LEU B:106 , SAH B:203BINDING SITE FOR RESIDUE EDO B 202
5AC5SOFTWAREALA A:116 , GLU A:117 , LEU B:78 , THR B:79 , PHE B:99 , GLY B:100 , PRO B:101 , GLU B:102 , GLY B:105 , ILE B:120 , ILE B:122 , MET B:124 , SER B:130 , MET B:131 , EDO B:202BINDING SITE FOR RESIDUE SAH B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:33 -Pro A:34
2Glu B:33 -Pro B:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JAL)

(-) 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:156
                                                                                                                                                                                            
               SCOP domains d4jala_ A: automated matches                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhhh.eee.hhhhhhhhhh..eeeee................eeeee.......hhhhhhh.hhh.ee...........hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jal A   0 MALNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVL 155
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149      


Chain B from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains d4jalb_ B: automated matches                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhh.eeeee.......hhhhhhhh..hhhhhhh.eee.hhhhhhhhhh..eeeee................eeeee.......hhhhhhh.hhh.ee...........hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jal B   0 MALNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAV 154
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRML_ECOLI | P0AGJ7: 4jak

(-) Related Entries Specified in the PDB File

4jak