3BT7 - JenaLib

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Title :   STRUCTURE OF E. COLI 5-METHYLURIDINE METHYLTRANSFERASE TRMA IN COMPLEX WITH 19 NUCLEOTIDE T-ARM ANALOGUE

Authors :   A. Alian, R. M. Stroud, J. Finer-Moore

Date :   27 Dec 07 (Deposition) - 29 Apr 08 (Release) - 25 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Methyluridine, Methyltransferase, Trma, Rumt, S-Adenosyl-L- Methionine, Trna Processing, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Alian, T. T. Lee, S. L. Griner, R. M. Stroud, J. Finer-Moore
Structure Of A Trma-Rna Complex: A Consensus Rna Fold Contributes To Substrate Selectivity And Catalysis In M5U Methyltransferases.
Proc. Natl. Acad. Sci. Usa V. 105 6876 2008
PubMed-ID: 18451029 | Reference-DOI: 10.1073/PNAS.0802247105

Molecule 1 - TRNA (URACIL-5-)-METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TRMA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRNAM-5-U54, METHYLTRANSFERASE, RUMT

*Molecule 2 - RNA (5'-D(PGPCPUPGPUPGP(5MU) PUPCPGPAPUPCPCPAPCPAPGPC)-3')**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	5MU	2	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	5MU	1	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	5MU	1	Mod. Nucleotide	5-METHYLURIDINE 5'-MONOPHOSPHATE

(no "Site" information available for 3BT7)

(no "SS Bond" information available for 3BT7)

(no "Cis Peptide Bond" information available for 3BT7)

(no "SAP(SNP)/Variant" information available for 3BT7)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RNA_M5U	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.	TRMA_ECOLI	2-366	2	A:2-366 B:2-366
2	TRMA_1	PS01230	RNA methyltransferase trmA family signature 1.	TRMA_ECOLI	299-328	2	A:299-328 B:299-328
3	TRMA_2	PS01231	RNA methyltransferase trmA family signature 2.	TRMA_ECOLI	348-358	2	A:348-357 B:348-357

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RNA_M5U	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.	TRMA_ECOLI	2-366	1	A:2-366 -
2	TRMA_1	PS01230	RNA methyltransferase trmA family signature 1.	TRMA_ECOLI	299-328	1	A:299-328 -
3	TRMA_2	PS01231	RNA methyltransferase trmA family signature 2.	TRMA_ECOLI	348-358	1	A:348-357 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RNA_M5U	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.	TRMA_ECOLI	2-366	1	- B:2-366
2	TRMA_1	PS01230	RNA methyltransferase trmA family signature 1.	TRMA_ECOLI	299-328	1	- B:299-328
3	TRMA_2	PS01231	RNA methyltransferase trmA family signature 2.	TRMA_ECOLI	348-358	1	- B:348-357

(no "Exon" information available for 3BT7)

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:369
 aligned with TRMA_ECOLI | P23003 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:369
                               1                                                                                                                                                                                                                                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
           TRMA_ECOLI     - ---MTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMECGVLLTAK 366
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh.......eee.........eeeeeeeee..eeeeeee......eee.......hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh...eeeeeeee..eeee....eeeee........eeeee.......hhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh....eeee...hhhhhhhhh......hhhhhhhhhh.eeeeee.......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhheeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----SAM_MT_RNA_M5U  PDB: A:2-366 UniProt: 2-366                                                                                                                                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRMA_1  PDB: A:299-328        -------------------TRMA_2     -------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bt7 A  -2 GSHMTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMQCGVLLTAK 366
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357

Chain B from PDB  Type:PROTEIN  Length:369
 aligned with TRMA_ECOLI | P23003 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:369
                               1                                                                                                                                                                                                                                                                                                                                                                             
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357         
           TRMA_ECOLI     - ---MTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMECGVLLTAK 366
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhh.......eee.........eeeeeeeee..eeeeeee......eee.......hhhhhhhhhhhhhhhh.hhhhhh.eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh...eeeeeeee..eeee....eeeee........eeeee.......hhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh....eeee...hhhhhhhhh......hhhhhhhhhh.eeeeee.......hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhheeeeeeeee.........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----SAM_MT_RNA_M5U  PDB: B:2-366 UniProt: 2-366                                                                                                                                                                                                                                                                                                                                   PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRMA_1  PDB: B:299-328        -------------------TRMA_2     -------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bt7 B  -2 GSHMTPEHLPTEQYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMQCGVLLTAK 366
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357

Chain C from PDB  Type:RNA  Length:19
                                                   
                 3bt7 C  48 GCUGUGuUCGAUCCACAGC  66
                                  | 57         
                                 54-5MU

Chain D from PDB  Type:RNA  Length:19
                                                   
                 3bt7 D  48 GCUGUGuUCGAUCCACAGC  66
                                  | 57         
                                 54-5MU

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

(no "SCOP Domain" information available for 3BT7)

(no "CATH Domain" information available for 3BT7)

(no "Pfam Domain" information available for 3BT7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRMA_ECOLI | P23003)

molecular function
	GO:0008173	RNA methyltransferase activity	Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
	GO:0030697	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing thymine at position U54 of a transfer RNA. This occurs in most Gram-negative bacteria, some archae, and eukaryotes.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
	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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	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: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: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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1uwv	5-METHYLURIDINE METHYLTRANSFERASE RUMA
2bh2	5-METHYLURIDINE METHYLTRANSFERASE RUMA IN COMPLEX WITH RNA AND SAM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Gene Ontology (11, 11)

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