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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A M1G37 TRNA METHYLTRANSFERASE, TRMD
 
Authors :  P. A. Elkins, J. M. Watts, M. Zalacain, A. Van Thiel, P. R. Vitaszka, M. R C. Andraos-Selim, F. Rastinejad, W. M. Holmes
Date :  12 May 03  (Deposition) - 18 May 04  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Knot, Methyltransferase, Adomet, S-Adenosylmethionine, Spou, Spout, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. A. Elkins, J. M. Watts, M. Zalacain, A. Van Thiel, P. R. Vitaszka, M. Redlak, C. Andraos-Selim, F. Rastinejad, W. M. Holmes
Insights Into Catalysis By A Knotted Trmd Trna Methyltransferase.
J. Mol. Biol. V. 333 931 2003
PubMed-ID: 14583191  |  Reference-DOI: 10.1016/J.JMB.2003.09.011

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TRMD OR B2607 OR C3128 OR Z3901 OR ECS3470 OR SF2667
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 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  (1, 1)

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR 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 , TRP A:131 , SER A:132 , ILE A:133 , GLY A:134 , TYR A:136 , LEU A:138 , GLY A:140 , GLY A:141 , PRO A:144 , ASP A:177 , HIS A:180 , HOH A:411 , HOH A:419BINDING SITE FOR RESIDUE SAH A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P9P)

(-) 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 1P9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P9P)

(-) Exons   (0, 0)

(no "Exon" information available for 1P9P)

(-) 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:235
 aligned with TRMD_ECOLI | P0A873 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           TRMD_ECOLI     1 MWIGIISLFPEMFRAITDYGVTGRAVKNGLLSIQSWSPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGIDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVSRFIPGVLGHEASATEDSFAEGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQ 246
               SCOP domains d1p9pa_ A: tRNA(m1G37)-methyltransferase TrmD                                                                                                                                                                                                          SCOP domains
               CATH domains 1p9pA01 A:1-160  [code=3.40.1280.10, no name defined]                                                                                                           1           p9pA02 A:161-246 tRNA(m1g37)methyltransferase, domain 2                    CATH domains
               Pfam domains ---------------------tRNA_m1G_MT-1p9pA01 A:22-221                                                                                                                                                                            ------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhh.......ee.........eehhhhhhhhhhhhhhhhh...eeeee....ee.hhhhhhhhhh..eeeee.......hhhhhhhhh.eeee........hhhhhhhhhhhhhh.......-----------.............ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p9p A   1 MWIGIISLFPEMFRAITDYGVTGRAVKNGLLSIQSWSPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGIDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVSRFIPGVLG-----------EGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRPELLENLALTEEQARLLAEFKTEHAQ 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|        -  |    180       190       200       210       220       230       240      
                                                                                                                                                                                          161         173
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  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  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMD_ECOLI | P0A873)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0002939    tRNA N1-guanine methylation    The process whereby a guanine in tRNA is methylated at position N1 of the guanine.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1p9p
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