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(-) Description

Title :  THE COMPLEX STRUCTURE OF ATRM5 AND TRNALEU
 
Authors :  S. Goto-Ito, T. Ito, S. Yokoyama
Date :  19 Feb 09  (Deposition) - 15 Sep 09  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goto-Ito, T. Ito, M. Kuratani, Y. Bessho, S. Yokoyama
Tertiary Structure Checkpoint At Anticodon Loop Modification In Trna Functional Maturation
Nat. Struct. Mol. Biol. V. 16 1109 2009
PubMed-ID: 19749755  |  Reference-DOI: 10.1038/NSMB.1653
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0883
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: METHANOCOCCUS JANNASCHII
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
 
Molecule 2 - RNA (84-MER)
    Chains: B
    Engineered: YES
    Other Details: SYNTHESIZED IN VITRO WITH THE RECOMBINANT RNA POLYMERASE OF T7 PHAGE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MG5Ligand/IonMAGNESIUM ION
2MLZ4Mod. Amino AcidN-METHYL-LYSINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:143 , PHE A:144 , TYR A:177 , PHE A:178 , SER A:179 , LEU A:182 , ARG A:186 , PHE A:203 , PRO A:208 , PHE A:209 , ASP A:223 , ILE A:224 , ASN A:225 , SER A:250 , ASP A:251 , VAL A:252 , ASN A:265 , LEU A:266 , HOH A:506 , HOH A:518 , G B:37BINDING SITE FOR RESIDUE SAM A 401
2AC2SOFTWAREC B:20A , A B:59 , HOH B:610BINDING SITE FOR RESIDUE MG B 101
3AC3SOFTWAREG B:47A , A B:47CBINDING SITE FOR RESIDUE MG B 102
4AC4SOFTWAREHOH B:612BINDING SITE FOR RESIDUE MG B 103
5AC5SOFTWAREU B:34BINDING SITE FOR RESIDUE MG B 105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZZM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZZM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM5_TYW2PS51684 SAM-dependent methyltransferase TRM5/TYW2-type domain profile.TRM5B_METJA97-335  1A:97-334

(-) Exons   (0, 0)

(no "Exon" information available for 2ZZM)

(-) 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:333
 aligned with TRM5B_METJA | Q58293 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:333
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          TRM5B_METJA     2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISKKYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLKKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVKSYAPREYILALDFKIN 334
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------Met_10-2zzmA01 A:95-289                                                                                                                                                                            --------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhh..............eeeee....hhhhhhhhh....................hhhhhhhhhhhhhhhh.......eee..eeee......hhhhhhhhhhhhhhhh...eeeee............eeeeee....eeeeee..eeeeee......hhhhhhhhhhhhh......eeee.....hhhhhh.....eeeeee.hhhhhhhhhhhhhhh.....eeeee.hhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhh...eeeeeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------SAM_MT_TRM5_TYW2  PDB: A:97-334 UniProt: 97-335                                                                                                                                                                                                PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zzm A   2 PLCLKINKKHGEQTRRILIENNLLNKDYKITSEGNYLYLPIKDVDEDILKSILNIEFELVDKELEEKKIIKKPSFREIISkkYRKEIDEGLISLSYDVVGDLVILQISDEVDEKIRKEIGELAYKLIPCKGVFRRKSEVKGEFRVRELEHLAGENRTLTIHKENGYRLWVDIAKVYFSPRLGGERARIMKKVSLNDVVVDMFAGVGPFSIACKNAKKIYAIDINPHAIELLkKNIKLNKLEHKIIPILSDVREVDVKGNRVIMNLPKFAHKFIDKALDIVEEGGVIHYYTIGKDFDKAIKLFEKKCDCEVLEKRIVkSYAPREYILALDFKIN 334
                                    11        21        31        41        51        61        71        81||      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 |     241       251       261       271       281       291       301       311      |321       331   
                                                                                                           82-MLZ                                                                                                                                                233-MLZ                                                                              318-MLZ            
                                                                                                            83-MLZ                                                                                                                                                                                                                                                       


Chain B from PDB  Type:RNA  Length:84
                                                                                                                    
                 2zzm B   1 GCAGGGGUCGCCAAGCCUGGCCAAAGGCGCUGGGCCUAGGACCCAGUCCCGUAGGGGUUCCAGGGUUCAAAUCCCUGCCCCUGC  72
                                    10       |19 ||     27        37        47||||||||48        58        68    
                                           17A 20A|                         47A||||||||                         
                                                20B                          47B|||||||                         
                                                                              47C||||||                         
                                                                               47D|||||                         
                                                                                47E||||                         
                                                                                 47F|||                         
                                                                                  47G||                         
                                                                                   47H|                         
                                                                                    47I
   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 2ZZM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRM5B_METJA | Q58293)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0052906    tRNA (guanine(37)-N(1))-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + guanine(37) in tRNA = N(1)-methylguanine(37) in tRNA + S-adenosyl-L-homocysteine.
    GO:0009019    tRNA (guanine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  2zzm
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  TRM5B_METJA | Q58293
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRM5B_METJA | Q58293: 2yx1 2zzn 3ay0

(-) Related Entries Specified in the PDB File

2zzn