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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRNA-GUANINE-N1-METHYLTRANSFERASE FROM MYCOBACTERIUM ABSCESSUS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  24 Feb 11  (Deposition) - 16 Mar 11  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sssgcid, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Trna Methyltransferase, Trmd, S-Adenosyl-Methionine, S- Adenosyl-Homocysteine, Sam, Sah, Chronic Lung Disease, Protein Knot, 3(1) Trefoil Knot, Domain Swap, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Phan, D. W. Begley, M. C. Clifton, B. Armour, D. M. Dranow, B. M. Taylor, M. M. Muruthi, J. Abendroth, J. W. Fairman, D. Fox, S. H. Dieterich, B. L. Staker, A. S. Gardberg, R. Choi, S. N. Hewitt, A. J. Napuli, J. Myers, L. K. Barrett, Y. Zhang, M. Ferrell, E. Mundt, K. Thompkins, N. Tran, S. Lyons-Abbott, A. Abramov, A. Sekar, D. Serbzhinskiy, D. Lorimer, G. W. Buchko, R. Stacy, L. J. Stewart, T. E. Edwards, W. C. Van Voorhis, P. J. Myler
Increasing The Structural Coverage Of Tuberculosis Drug Targets.
Tuberculosis (Edinb) V. 95 142 2015
PubMed-ID: 25613812  |  Reference-DOI: 10.1016/J.TUBE.2014.12.003

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Atcc: 19977
    Chains: A, B
    EC Number: 2.1.1.31
    Engineered: YES
    Gene: MAB_3226C, TRMD
    Organism Scientific: MYCOBACTERIUM ABSCESSUS
    Organism Taxid: 561007
    Strain: DSM 44196
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:84 , PRO A:85 , LEU A:138 , GLY A:140 , GLY A:141 , HOH A:282 , HOH A:352 , HOH A:358BINDING SITE FOR RESIDUE EDO A 243
2AC2SOFTWAREVAL A:82 , PRO A:83 , THR A:84 , ARG A:110 , GLY A:113 , ILE A:114 , HOH A:342BINDING SITE FOR RESIDUE EDO A 244
3AC3SOFTWARETHR B:84 , PRO B:85 , LEU B:138 , GLY B:140 , HOH B:249 , HOH B:306 , HOH B:323 , HOH B:382BINDING SITE FOR RESIDUE EDO B 243
4AC4SOFTWAREASP A:71 , LEU A:200 , SER A:201 , HOH A:384 , ARG B:191BINDING SITE FOR RESIDUE EDO A 245

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:186 -Pro A:187
2Arg B:186 -Pro B:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QUV)

(-) 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:216
 aligned with B1MDI3_MYCA9 | B1MDI3 from UniProtKB/TrEMBL  Length:242

    Alignment length:229
                              1                                                                                                                                                                                                                                  
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218         
         B1MDI3_MYCA9     - --MKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNALSAQEDSHSEGMASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLL 227
               SCOP domains d3quva_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhhhhhhhh.hhhhhhh..eeeeeee.hhhh.......ee.........eehhhhhhhhhhhhh....eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhhh...eeeeee........hhhhhhhhhhhhhh.........-------------............ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3quv A  -1 GSMKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNA-------------SLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLL 227
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    |    -       178       188       198       208       218         
                                                                                                                                                                                              163           177                                                  


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with B1MDI3_MYCA9 | B1MDI3 from UniProtKB/TrEMBL  Length:242

    Alignment length:232
                             1                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
         B1MDI3_MYCA9     - -MKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNALSAQEDSHSEGMASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLLGFDS 231
               SCOP domains d3quvb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------tRNA_m1G_MT-3quvB01 B:21-224                                                                                                                                                                                ------- Pfam domains (1)
           Pfam domains (2) ---------------------tRNA_m1G_MT-3quvB02 B:21-224                                                                                                                                                                                ------- Pfam domains (2)
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh.......ee.........eehhhhhhhhhhhhh....eeeee....ee.hhhhhhhhh...eeeee........hhhhhhhhh..eeeeee........hhhhhhhhhhhhhh.hhhhhhhhhhh---------.............ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3quv B   0 SMKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVLGNALSA---------ASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLLGFDS 231
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159      |  -      |179       189       199       209       219       229  
                                                                                                                                                                                                166       176
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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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B1MDI3_MYCA9 | B1MDI3)
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: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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