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(-) Description

Title :  CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
 
Authors :  M. Fislage, M. Roovers, I. Tuszynska, J. M. Bujnicki, L. Droogmans, W. V
Date :  30 Aug 11  (Deposition) - 14 Mar 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold, Methyltransferase, Thump Domain, Trna Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fislage, M. Roovers, I. Tuszynska, J. M. Bujnicki, L. Droogmans, W. Versees
Crystal Structures Of The Trna:M2G6 Methyltransferase Trm14/Trmn From Two Domains Of Life.
Nucleic Acids Res. V. 40 5149 2012
PubMed-ID: 22362751  |  Reference-DOI: 10.1093/NAR/GKS163

(-) Compounds

Molecule 1 - TRNA (GUANINE N2-)-METHYLTRANSFERASE TRM14
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF1002
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: ATCC 43587 / DSM 3638 / JCM 8422 / VC1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:198 , ALA A:200 , HIS A:201 , LEU A:202 , MET A:225 , CYS A:226 , GLY A:227 , SER A:228 , GLY A:229 , THR A:230 , GLU A:248 , LYS A:249 , TYR A:250 , HIS A:253 , GLY A:275 , ASP A:276 , ALA A:277 , ASN A:293 , LEU A:309BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWAREASP A:217 , ARG A:324BINDING SITE FOR RESIDUE ACT A 402
3AC3SOFTWAREHIS B:198 , ALA B:200 , HIS B:201 , LEU B:202 , PRO B:224 , MET B:225 , CYS B:226 , GLY B:227 , SER B:228 , GLY B:229 , THR B:230 , GLU B:248 , TYR B:250 , HIS B:253 , GLY B:275 , ASP B:276 , ALA B:277 , ASN B:293 , HOH B:644BINDING SITE FOR RESIDUE SAH B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TLJ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TLJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TLJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TLJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3TLJ)

(-) 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    
   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:364
 aligned with Q8U248_PYRFU | Q8U248 from UniProtKB/TrEMBL  Length:365

    Alignment length:370
                                                                                                                                                                                                                                                                                                                                                                                                      365     
                                    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       320       330       340       350       360    |    -
         Q8U248_PYRFU     1 MKFLLTTAQGIEDIAKREVSLLLKKLGISFQIEEKPLGIEGRLLLEAEKAYYVDEKGRKRELSISTYLNENSRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRAELIKDVFFLGIDTTGDSSLHKRPWRVYDHPAHLKASIANAMIELAELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAISNLPYGLKIGKKSMIPDLYMKFFNELAKVLEKRGVFITTEKKAIEEAIAENGFEIIHHRVIGHGGLMVHLYVVK-----   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhhh..eeeee.hhhh..eeeeee..eeee.....eeeehhhhhhhhhh....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhh.....ee......eeeeeeee..eeeeeee.....................hhhhhhhhhhhhh.....eee.....hhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhheeee.hhhhhhhhh..eeeeeee....------.hhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhh.eeeeeeeeee....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tlj A   1 MKFLLTTAQGIEDIAKREVSLLLKKLGISFQIEEKPLGIEGRLLLEAEKAYYVDEKGRKRELSISTYLNENSRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRAELIKDVFFLGIDTTGDSSLHKRPWRVYDHPAHLKASIANAMIELAELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAISNLPYG------SMIPDLYMKFFNELAKVLEKRGVFITTEKKAIEEAIAENGFEIIHHRVIGHGGLMVHLYVVKLEHHH 370
                                    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      |  -   |   310       320       330       340       350       360       370
                                                                                                                                                                                                                                                                                                                                  297    304                                                                  


Chain B from PDB  Type:PROTEIN  Length:364
 aligned with Q8U248_PYRFU | Q8U248 from UniProtKB/TrEMBL  Length:365

    Alignment length:370
                                                                                                                                                                                                                                                                                                                                                                                                      365     
                                    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       320       330       340       350       360    |    -
         Q8U248_PYRFU     1 MKFLLTTAQGIEDIAKREVSLLLKKLGISFQIEEKPLGIEGRLLLEAEKAYYVDEKGRKRELSISTYLNENSRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRAELIKDVFFLGIDTTGDSSLHKRPWRVYDHPAHLKASIANAMIELAELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAISNLPYGLKIGKKSMIPDLYMKFFNELAKVLEKRGVFITTEKKAIEEAIAENGFEIIHHRVIGHGGLMVHLYVVK-----   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhhhh...eeeee.hhhh..eeeeee..eeee.....eeeehhhhhhhhhh....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....hhhhhhhhhhhhhhhhhh.....ee......eeeeeeee..eeeeeee.....................hhhhhhhhhhhh......eee.....hhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhh...eeeeeee....------.hhhhhhhhhhhhhhhheeeeeeeee.hhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tlj B   1 MKFLLTTAQGIEDIAKREVSLLLKKLGISFQIEEKPLGIEGRLLLEAEKAYYVDEKGRKRELSISTYLNENSRLLHRVIIEIASEKFNGIEKDESEEALKRIKDFVSSLPVEQFVKVSETFAVRSFRKGDHNITSIDIARTVGEAIFERLSRFGTPLVNLDHPAVIFRAELIKDVFFLGIDTTGDSSLHKRPWRVYDHPAHLKASIANAMIELAELDGGSVLDPMCGSGTILIELALRRYSGEIIGIEKYRKHLIGAEMNALAAGVLDKIKFIQGDATQLSQYVDSVDFAISNLPYG------SMIPDLYMKFFNELAKVLEKRGVFITTEKKAIEEAIAENGFEIIHHRVIGHGGLMVHLYVVKLEHHH 370
                                    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      |  -   |   310       320       330       340       350       360       370
                                                                                                                                                                                                                                                                                                                                  297    304
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 3TLJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TLJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TLJ)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8U248_PYRFU | Q8U248)
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:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8U248_PYRFU | Q8U248: 3tm4 3tm5

(-) Related Entries Specified in the PDB File

3tm4 3tm5 3tma