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(-) Description

Title :  COMPLEX STRUCTURE OF TRM1 FROM PYROCOCCUS HORIKOSHII WITH S-ADENOSYL-L-HOMOCYSTEIN
 
Authors :  Ihsanawati, M. Shirouzu, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Mar 07  (Deposition) - 25 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Trna Modification Enzyme, Guanine-26, N(2)-N(2)-Dimethyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Ihsanawati, M. Nishimoto, K. Higashijima, M. Shirouzu, H. Grosjean, Y. Bessho, S. Yokoyama
Crystal Structure Of Trna N(2), N(2)-Guanosine Dimethyltransferase Trm1 From Pyrococcus Horikoshii
J. Mol. Biol. V. 383 871 2008
PubMed-ID: 18789948  |  Reference-DOI: 10.1016/J.JMB.2008.08.068

(-) Compounds

Molecule 1 - N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE
    ChainsA
    EC Number2.1.1.32
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System StrainBL21-CODONPLUS (DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-378
    GeneTRM1
    MutationYES
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid53953
    SynonymTRNA(GUANINE-26,N(2)-N(2))METHYLTRANSFERASE, TRNA 2,2- DIMETHYLGUANOSINE-26 METHYLTRANSFERASE, TRNA(M(2,2)G26) DIMETHYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:36 , LEU A:55 , ALA A:57 , ILE A:60 , ARG A:61 , ASN A:77 , ASP A:78 , ILE A:79 , SER A:80 , ASP A:119 , ASP A:120 , ALA A:121 , ASP A:138 , PHE A:140 , PHE A:146 , HOH A:618 , HOH A:623 , HOH A:640 , HOH A:750 , HOH A:795 , HOH A:864 , HOH A:894BINDING SITE FOR RESIDUE SAH A 501
2AC2SOFTWAREALA A:220 , LEU A:281 , LYS A:282 , ILE A:312 , GLU A:315 , LEU A:316 , ASP A:317 , HIS A:356 , HOH A:642BINDING SITE FOR RESIDUE GOL A 601

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:171 -A:192

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:274 -Pro A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EJU)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  1A:4-375
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  1A:4-375
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  2A:4-375

(-) Exons   (0, 0)

(no "Exon" information available for 2EJU)

(-) 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:371
 aligned with TRM1_PYRHO | O59493 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:375
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375     
           TRM1_PYRHO     6 LIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 380
               SCOP domains d2ejua_ A: N(2),    N(2)-dimethylguanosine tRNA methyltransferase Trm1                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee...----......hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......ee...eeeee...eeeeee.hhhhhhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeee.hhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhh.eeeeee......eeeee.........eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eehhhhhhhhh....hhhhhhhhhhhh...eeee..eeeeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_MT_TRM1  PDB: A:4-375 UniProt: 7-378                                                                                                                                                                                                                                                                                                                                            -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eju A   3 LIEVQEGKAKILIPKA----DSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 377
                                    12     |   -|       32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
                                          18   23                                                                                                                                                                                                                                                                                                                                                                  

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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2EJU)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EJU)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRM1_PYRHO | O59493)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004809    tRNA (guanine-N2-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRM1_PYRHO | O594932dul 2ejt 2ytz

(-) Related Entries Specified in the PDB File

2dul THE SAME PROTEIN BUT WITHOUT LIGAND
2ejt THE SAME PROTEIN WITH S-ADENOSYL-L-METHIONINE RELATED ID: PHO001001829.3 RELATED DB: TARGETDB