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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA(M1G37)METHYLTRANSFERASE: INSIGHT INTO TRNA RECOGNITION
 
Authors :  H. J. Ahn, H. -W. Kim, H. -J. Yoon, B. I. Lee, S. W. Suh, J. K. Yang
Date :  11 Mar 03  (Deposition) - 17 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Methyltransferase, Spout Class, Trmd, Trna(M1G37)Methyltransferase, Trna Modification, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Ahn, H. -W. Kim, H. -J. Yoon, B. I. Lee, S. W. Suh, J. K. Yang
Crystal Structure Of Trna(M(1)G37)Methyltransferase: Insights Into Trna Recognition
Embo J. V. 22 2593 2003
PubMed-ID: 12773376  |  Reference-DOI: 10.1093/EMBOJ/CDG269

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: TRNA(M1G37)METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:9 , GLY A:20 , VAL A:21 , ARG A:24 , ARG A:114 , TYR A:115BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWARETYR A:86 , LEU A:87 , SER A:88 , PRO A:89 , GLN A:90 , GLY A:113 , TYR A:115 , GLU A:116 , GLY A:117 , SER A:132 , ILE A:133 , GLY A:134 , TYR A:136 , VAL A:137 , LEU A:138 , THR A:139 , GLY A:140 , GLY A:141 , PRO A:144 , ASP A:169 , SER A:170 , ASP A:177 , HOH A:1032BINDING SITE FOR RESIDUE SAH A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UAM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UAM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UAM)

(-) Exons   (0, 0)

(no "Exon" information available for 1UAM)

(-) 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:250
 aligned with TRMD_HAEIN | P43912 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:252
                              1                                                                                                                                                                                                                                                  246    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       | -  
           TRMD_HAEIN     - --MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS----   -
               SCOP domains d1uama_ A: tRNA(m1G37)-methyltransferase TrmD                                                                                                                                                                                                                SCOP domains
               CATH domains 1uamA01 A:-1-160  [code=3.40.1280.10, no name defined]                                                                                                            ---------1uamA02 A:170-250 tRNA(m1g37)methyltransferase, domain 2                          CATH domains
               Pfam domains -----------------------tRNA_m1G_MT-1uamA01 A:22-221                                                                                                                                                                            ----------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh.........--....................ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1uam A  -1 SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLIDAVARFIPGVLGKQ--AEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNSLEHH 250
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    |  168       178       188       198       208       218       228       238       248  
                                                                                                                                                                                              163  |                                                                                    
                                                                                                                                                                                                 166
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMD_HAEIN | P43912)
molecular function
    GO:0008685    2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        TRMD_HAEIN | P43912: 1uaj 1uak 1ual 3axz 4mcb 4mcc 4mcd 4ypw 4ypx 4ypy 4ypz 4yq0 4yq1 4yq2 4yq3 4yq4 4yq5 4yq6 4yq7 4yq8 4yq9 4yqa 4yqb 4yqc 4yqd 4yqg 4yqi 4yqj 4yqk 4yql 4yqn 4yqo 4yqp 4yqq 4yqr 4yqs 4yqt 4yvg 4yvh 4yvi 4yvj 4yvk 5d9f

(-) Related Entries Specified in the PDB File

1uaj TRNA(M1G37)METHYLTRANSFERASE
1uak TRNA(M1G37)METHYLTRANSFERASE WITH S-ADENOSYLMETHIONINE
1ual TRNA(M1G37)METHYLTRANSFERASE WITH S-ADENOSYL-L-HOMOCYSTEINE