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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE CMOA FROM E.COLI
 
Authors :  J. Kim, R. Toro, J. B. Bonanno, R. Bhosle, P. Sampathkumar, S. C. Almo, Ne Structural Genomics Research Consortium (Nysgrc)
Date :  02 Aug 12  (Deposition) - 10 Oct 12  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,G
Keywords :  Structural Genomics, Psi-Biology, New York Structural Genomics Research Consortium, Nysgrc, Rossmann Fold, Synthase, Sam Prephenate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kim, H. Xiao, J. B. Bonanno, C. Kalyanaraman, S. Brown, X. Tang, N. F. Al-Obaidi, Y. Patskovsky, P. C. Babbitt, M. P. Jacobson, Y. -S. Lee, S. C. Almo
Structure-Guided Discovery Of The Metabolite Carboxy-Sam That Modulates Trna Function
Nature V. 498 123 2013
PubMed-ID: 23676670  |  Reference-DOI: 10.1038/NATURE12180

(-) Compounds

Molecule 1 - TRNA (CMO5U34)-METHYLTRANSFERASE
    ChainsA, G
    EC Number2.1.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidLIC PET46A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCMOA
    Organism ScientificESCHERICHIA COLI
    Organism Taxid511145
    StrainK-12 SUBSTR. MG1655

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1GEK2Ligand/Ion(2S)-4-[{[(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}(CARBOXYLATOMETHYL)SULFONIO]-2-AMMONIOBUTANOATE
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:69 , ARG A:76 , HIS A:101 , HOH A:419 , HOH A:446 , HOH A:451 , HOH A:582 , HOH A:588BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREPHE A:20 , PHE A:28 , TYR A:39 , GLY A:64 , SER A:66 , ASP A:89 , ASN A:90 , SER A:91 , MET A:94 , GLY A:116 , ASP A:117 , ILE A:118 , ASN A:132 , PHE A:133 , PHE A:137 , LEU A:138 , ARG A:199 , HOH A:401 , HOH A:403 , HOH A:406 , HOH A:417 , HOH A:444 , HOH A:610BINDING SITE FOR RESIDUE GEK A 302
3AC3SOFTWARELYS A:172 , HIS G:225 , ALA G:243 , GLU G:244 , HOH G:546BINDING SITE FOR RESIDUE SO4 G 301
4AC4SOFTWAREALA G:69 , ARG G:76 , HIS G:101 , HOH G:423 , HOH G:429 , HOH G:525 , HOH G:561BINDING SITE FOR RESIDUE SO4 G 302
5AC5SOFTWAREPHE G:20 , PHE G:28 , TYR G:39 , GLY G:64 , SER G:66 , ASP G:89 , ASN G:90 , SER G:91 , MET G:94 , GLY G:116 , ASP G:117 , ILE G:118 , ASN G:132 , PHE G:133 , PHE G:137 , LEU G:138 , ARG G:199 , HOH G:401 , HOH G:402 , HOH G:405 , HOH G:414 , HOH G:563 , HOH G:585BINDING SITE FOR RESIDUE GEK G 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GEK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GEK)

(-) 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:230
                                                                                                                                                                                                                                                                      
               SCOP domains d4geka_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh......eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gek A  18 WTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVLNFTLQFLEPSERQALLDKIYQGLNPGGALVLSEKFSFEDAKVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQCFNFGSLVALKAEDAA 247
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

Chain G from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                       
               SCOP domains d4gekg_ G: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhh......eeeee..........eeeeeee.hhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..eeeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gek G  15 LGDWTFDERVAEVFPDMIQRSVPGYSNIISMIGMLAERFVQPGTQVYDLGCSLGAATLSVRRNIHHDNCKIIAIDNSPAMIERCRRHIDAYKAPTPVDVIEGDIRDIAIENASMVVLNFTLQFLEPSERQALLDKIYQGLNPGGALVLSEKFSFEDAKVGELLFNMHHDFKRANGYSELEISQKRSMLENVMLTDSVETHKARLHKAGFEHSELWFQCFNFGSLVALKAED 245
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244 

   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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        CMOA_ECOLI | P762904iwn

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