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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

Ligands, Modified Residues, Ions (4, 9)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
3	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
4	THG	1	Ligand/Ion	(6S)-5,6,7,8-TETRAHYDROFOLATE

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY 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:557	BINDING SITE FOR RESIDUE FAD A 444
2	AC2	SOFTWARE	PRO A:135 , HIS A:308 , ARG A:309 , ASN A:310 , FAD A:444 , HOH A:612 , HOH A:812 , HOH A:813	BINDING SITE FOR RESIDUE THG A 445
3	AC3	SOFTWARE	LEU A:84 , HOH A:512 , HOH A:556 , HOH A:739 , HOH A:740	BINDING SITE FOR RESIDUE CA A 446
4	AC4	SOFTWARE	HIS A:152 , PHE A:153 , ASN A:314 , PHE A:390 , HOH A:567 , HOH A:679	BINDING SITE FOR RESIDUE EDO A 447
5	AC5	SOFTWARE	ILE A:301 , VAL A:302 , TYR A:304 , TYR A:394 , ASN A:396 , HOH A:507 , HOH A:620	BINDING SITE FOR RESIDUE EDO A 448
6	AC6	SOFTWARE	LYS A:360 , GLY A:363 , PRO A:365 , HOH A:539 , HOH A:677	BINDING SITE FOR RESIDUE EDO A 449
7	AC7	SOFTWARE	PHE A:325 , ARG A:326 , GLU A:329	BINDING SITE FOR RESIDUE EDO A 450
8	AC8	SOFTWARE	LYS A:35 , MET A:37 , PHE A:175 , ARG A:176	BINDING SITE FOR RESIDUE EDO A 451
9	AC9	SOFTWARE	GLU A:265 , THR A:384 , ALA A:385 , ASN A:386 , HOH A:810	BINDING SITE FOR RESIDUE EDO A 452

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GIDA_2	PS01281	Glucose inhibited division protein A family signature 2.	TRMFO_THET8	334-357	1	A:334-357

Exons (0, 0)

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

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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

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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