Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH S-ADENOSYLMETHIONINE
 
Authors :  M. Fislage, M. Roovers, I. Tuszynska, J. M. Bujnicki, L. Droogmans, W. V
Date :  31 Aug 11  (Deposition) - 14 Mar 12  (Release) - 03 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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: PET30
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:198 , ALA A:200 , HIS A:201 , LEU A:202 , PRO A:224 , MET A:225 , CYS A:226 , GLY A:227 , SER A:228 , 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:309 , HOH A:635BINDING SITE FOR RESIDUE SAM A 401
2AC2SOFTWAREHIS 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 , THR B:230 , GLU B:248 , LYS B:249 , TYR B:250 , HIS B:253 , GLY B:275 , ASP B:276 , ALA B:277 , ASN B:293 , HOH B:544 , HOH B:579BINDING SITE FOR RESIDUE SAM B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TM4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TM4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TM4)

(-) Exons   (0, 0)

(no "Exon" information available for 3TM4)

(-) 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....hhhhhhhhhhhhhhh....eeeee.hhhh..eeeeee..eeee.....eeeehhhhhhhhhh....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....hhhhhhhhhhhhhhhhhhh....ee......eeeeeeee..eeeeeee.....................hhhhhhhhhhhhh.....eee.....hhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh.hhhhheeee.hhhhhhhh...eeeeeee....------.hhhhhhhhhhhhhhhheeeeeeeee.hhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tm4 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....hhhhhhhhhhhhhhh....eeeee.hhhh..eeeeee..eeee.....eeeehhhhhhhhhh....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....hhhhhhhhhhhhhhhhhhh....ee......eeeeeeee..eeeeeee.....................hhhhhhhhhhhh......eee.....hhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhh...eeeeeee....------.hhhhhhhhhhhhhhhheeeeeeeee.hhhhhhhhhhhh.eeeeeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tm4 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 3TM4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TM4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TM4)

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tm4)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tm4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8U248_PYRFU | Q8U248
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8U248_PYRFU | Q8U248
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8U248_PYRFU | Q8U248: 3tlj 3tm5

(-) Related Entries Specified in the PDB File

3tlj CRYSTAL STRUCTURE OF TRM14 FROM PYROCOCCUS FURIOSUS IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE
3tm5
3tma