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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS TRMFO IN COMPLEX WITH TETRAHYDROFOLATE
 
Authors :  H. Nishimasu, R. Ishitani, H. Hori, O. Nureki
Date :  05 Feb 09  (Deposition) - 19 May 09  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Trna Methyltransferase Fad Folate, Fad, Flavoprotein, Methyltransferase, Transferase, Trna Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Nishimasu, R. Ishitani, K. Yamashita, C. Iwashita, A. Hirata, H. Hori, O. Nureki
Atomic Structure Of A Folate/Fad-Dependent Trna T54 Methyltransferase
Proc. Natl. Acad. Sci. Usa V. 106 8180 2009
PubMed-ID: 19416846  |  Reference-DOI: 10.1073/PNAS.0901330106

(-) Compounds

Molecule 1 - METHYLENETETRAHYDROFOLATE--TRNA-(URACIL-5-)- METHYLTRANSFERASE TRMFO
    Chains: A
    EC Number: 2.1.1.74
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRMFO, TTHA1442
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: TRMFO, FOLATE-DEPENDENT TRNA (URACIL-5-)-METHYLTRANSFERASE, FOLATE-DEPENDENT TRNA(M-5-U54)-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4THG1Ligand/Ion(6S)-5,6,7,8-TETRAHYDROFOLATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:8 , GLY A:10 , LEU A:11 , ALA A:12 , GLU A:31 , MET A:32 , ARG A:33 , HIS A:41 , CYS A:51 , SER A:52 , GLU A:119 , GLU A:120 , VAL A:121 , ALA A:132 , THR A:133 , GLY A:134 , PRO A:135 , SER A:138 , GLY A:335 , VAL A:336 , GLY A:342 , TYR A:343 , SER A:346 , THG A:445 , HOH A:453 , HOH A:460 , HOH A:461 , HOH A:466 , HOH A:476 , HOH A:480 , HOH A:522 , HOH A:557BINDING SITE FOR RESIDUE FAD A 444
2AC2SOFTWAREPRO A:135 , HIS A:308 , ARG A:309 , ASN A:310 , FAD A:444 , HOH A:612 , HOH A:812 , HOH A:813BINDING SITE FOR RESIDUE THG A 445
3AC3SOFTWARELEU A:84 , HOH A:512 , HOH A:556 , HOH A:739 , HOH A:740BINDING SITE FOR RESIDUE CA A 446
4AC4SOFTWAREHIS A:152 , PHE A:153 , ASN A:314 , PHE A:390 , HOH A:567 , HOH A:679BINDING SITE FOR RESIDUE EDO A 447
5AC5SOFTWAREILE A:301 , VAL A:302 , TYR A:304 , TYR A:394 , ASN A:396 , HOH A:507 , HOH A:620BINDING SITE FOR RESIDUE EDO A 448
6AC6SOFTWARELYS A:360 , GLY A:363 , PRO A:365 , HOH A:539 , HOH A:677BINDING SITE FOR RESIDUE EDO A 449
7AC7SOFTWAREPHE A:325 , ARG A:326 , GLU A:329BINDING SITE FOR RESIDUE EDO A 450
8AC8SOFTWARELYS A:35 , MET A:37 , PHE A:175 , ARG A:176BINDING SITE FOR RESIDUE EDO A 451
9AC9SOFTWAREGLU A:265 , THR A:384 , ALA A:385 , ASN A:386 , HOH A:810BINDING SITE FOR RESIDUE EDO A 452

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G5R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:33 -Pro A:34
2Asn A:432 -Pro A:433

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G5R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GIDA_2PS01281 Glucose inhibited division protein A family signature 2.TRMFO_THET8334-357  1A:334-357

(-) Exons   (0, 0)

(no "Exon" information available for 3G5R)

(-) 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:420
 aligned with TRMFO_THET8 | Q5SID2 from UniProtKB/Swiss-Prot  Length:443

    Alignment length:436
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      
          TRMFO_THET8     1 MERVNVVGAGLAGSEAAWTLLRLGVPVRLFEMRPKRMTPAHGTDRFAEIVCSNSLGGEGETNAKGLLQAEMRRAGSLVMEAADLARVPAGGALAVDREEFSGYITERLTGHPLLEVVREEVREIPPGITVLATGPLTSEALAEALKRRFGDHFLAYYDAASPIVLYESIDLTKCFRAGRYGQSADYLNCPMTEEEYRRFHQALLEAQRHTPHDWEKLEFFEACVPVEELARRGYQTLLFGPMKPVGLVDPRTGKEPFAVVQLRQEDKAGRMWSLVGFQTGLKWPEQKRLIQMIPGLENAEIVRYGVMHRNTYLNAPRLLGETLEFREAEGLYAAGVLAGVEGYLESAATGFLAGLNAARKALGLPPVAPPEESMLGGLVRYLATANPEGFQPMYANWGLVPPVEGRMGKKEKRQAMYRRGLEAFSAWLSGLNPPLP 436
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhh...eeee.......................eeee....hhhhhhhhhhhhh.hhhhhhhhhhee....eeeehhhhhhhhhhhhhhh...eeee...........eee......hhhhhhhhhhhhh...eeeeeee..eee.hhhhhhhhee..........eeeeehhhhhhhhhhhhhhh----------------..hhhhhhhhh.hhhhhh.................eeeeeee......eeee.......hhhhhhhhhh.........eee..eeeeeeeehhhhhh...........eee.hhhhh..hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh..........hhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GIDA_2  PDB: A:334-357  ------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g5r A   1 MERVNVVGAGLAGSEAAWTLLRLGVPVRLFEMRPKRMTPAHGTDRFAEIVCSNSLGGEGETNAKGLLQAEMRRAGSLVMEAADLARVPAGGALAVDREEFSGYITERLTGHPLLEVVREEVREIPPGITVLATGPLTSEALAEALKRRFGDHFLAYYDAASPIVLYESIDLTKCFRAGRYGQSADYLNCPMTEEEYRRFHQALLEA----------------CVPVEELARRGYQTLLFGPMKPVGLVDPRTGKEPFAVVQLRQEDKAGRMWSLVGFQTGLKWPEQKRLIQMIPGLENAEIVRYGVMHRNTYLNAPRLLGETLEFREAEGLYAAGVLAGVEGYLESAATGFLAGLNAARKALGLPPVAPPEESMLGGLVRYLATANPEGFQPMYANWGLVPPVEGRMGKKEKRQAMYRRGLEAFSAWLSGLNPPLP 436
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     |   -         -  |    230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430      
                                                                                                                                                                                                                                       206              223
   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  (0, 0)

(no "SCOP Domain" information available for 3G5R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G5R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G5R)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TRMFO_THET8 | Q5SID2)
molecular function
    GO:0030698    5,10-methylenetetrahydrofolate-dependent tRNA (m5U54) methyltransferase activity    Catalysis of the transfer of a methyl group from 5,10-methylenetetrahydrofolate to the C5 atom of the uridine residue at position 54 in a tRNA molecule. This occurs in most Gram-positive bacteria and some Gram-negative bacteria.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0047151    methylenetetrahydrofolate-tRNA-(uracil-5-)-methyltransferase (FADH2-oxidizing) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + tRNA containing uridine at position 54 + FADH + H+ = tetrahydrofolate + tRNA containing ribothymidine at position 54 + FAD+.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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
        TRMFO_THET8 | Q5SID2: 3g5q 3g5s

(-) Related Entries Specified in the PDB File

3g5q THE SAME PROTEIN AT 2.1 A RESOLUTION
3g5s THE SAME PROTEIN AT 1.05 A RESOLUTION