3M6U - JenaLib

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Title :   MULTI-SITE-SPECIFIC 16S RRNA METHYLTRANSFERASE RSMF FROM THERMUS THERMOPHILUS IN SPACE GROUP 43

Authors :   H. Demirci, H. G. L. Larsen, T. Hansen, A. Rasmussen, A. Cadambi, S. T. Gr F. Kirpekar, G. Jogl

Date :   16 Mar 10 (Deposition) - 31 Mar 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Rrna Methyltransferase, 5-Methylcytidine, Rsmf, Adomet, Multi- Specific, Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Demirci, L. H. Larsen, T. Hansen, A. Rasmussen, A. Cadambi, S. T. Gregory, F. Kirpekar, G. Jogl
Multi-Site-Specific 16S Rrna Methyltransferase Rsmf From Thermus Thermophilus.
Rna V. 16 1584 2010
PubMed-ID: 20558545 | Reference-DOI: 10.1261/RNA.2088310

Molecule 1 - RRNA METHYLASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLJ102
	Expression System Strain	:	CP79
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TTHA1387
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:100 , ARG A:173 , ARG A:296 , ARG A:298 , HOH A:467 , HOH A:587 , HOH A:607 , HOH A:650 , HOH B:521 , HOH B:1204 , HOH B:1246	BINDING SITE FOR RESIDUE SO4 A 465
2	AC2	SOFTWARE	GLN A:86 , ALA A:90 , GLY A:114 , LYS A:115 , HOH A:634 , HOH A:705 , HOH A:1187 , HOH A:1214	BINDING SITE FOR RESIDUE SO4 A 466
3	AC3	SOFTWARE	HOH A:795 , HOH A:1310 , LYS B:100 , ARG B:173 , ARG B:296 , ARG B:298 , HOH B:476 , HOH B:634 , HOH B:693 , HOH B:754 , HOH B:1238	BINDING SITE FOR RESIDUE SO4 B 465
4	AC4	SOFTWARE	GLN B:86 , ALA B:90 , GLY B:114 , LYS B:115 , HOH B:524 , HOH B:641 , HOH B:741 , HOH B:1422	BINDING SITE FOR RESIDUE SO4 B 466

(no "SS Bond" information available for 3M6U)

Asymmetric Unit

No.	Residues
1	Ala A:111	-	Pro A:112
2	Ala B:111	-	Pro B:112

(no "SAP(SNP)/Variant" information available for 3M6U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RSMB_NOP	PS51686	SAM-dependent MTase RsmB/NOP-type domain profile.	RSMF_THET8	10-300	2	A:10-300 B:10-300

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RSMB_NOP	PS51686	SAM-dependent MTase RsmB/NOP-type domain profile.	RSMF_THET8	10-300	1	A:10-300 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_MT_RSMB_NOP	PS51686	SAM-dependent MTase RsmB/NOP-type domain profile.	RSMF_THET8	10-300	1	- B:10-300

(no "Exon" information available for 3M6U)

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:438
 aligned with RSMF_THET8 | Q5SII2 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             456   
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454 |   
           RSMF_THET8     5 AFLSRMAELLGEEFPAFLKALTEGKRTYGLRVNTLKLPPEAFQRISPWPLRPIPWCQEGFYYPEEARPGPHPFFYAGLYYIQEPSAQAVGVLLDPKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALAEAFGTYFHRVLLDAPCSGEGMFRKDREAARHWGPSAPKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAHPEFRLEDARLHPLFAPGVPEWGEGNPELLKTARLWPHRLEGEGHFLARFRKEGGAWSTPRLERPSPLSQEALRAFRGFLEEAGLTLEGPVLDRAGHLYLLPEGLPTLLGLKAPAPGLYLGKVQKGRFLPARALALAFGATLPWPEGLPRLALTPEDPRALAFATGEGVAWEGEDHPLALVVLKTAAGEFPLDFGKAKRGVLRPVGVGL---   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.hhhhhhhhhhh.....eeee.....hhhhhhhhh....ee......eee.........hhhhhh..eee..hhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh..eeeeeee.---------------.ee..--..hhhhhhhhhhhhhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhh..eeee........ee.hhhhh..hhhhhh.eee.........eeeeeeee................hhhhhhhhhhhhhhhh......eeee..eeee...........eeee..eeeeeee..eeeehhhhhhhh...........eeee...hhhhhhhhh...ee.....eeeeeeeeee..eeeeeeeeeee..eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_MT_RSMB_NOP  PDB: A:10-300 UniProt: 10-300                                                                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m6u A   5 AFLSRMAELLGEEFPAFLKALTEGKRTYGLRVNTLKLPPEAFQRISPWPLRPIPWCQEGFYYPEEARPGPHPFFYAGLYYIQEPSAQAVGVLLDPKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALAEAFGTYFHRVLLDA---------------RHWGP--PKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAHPEFRLEDARLHPLFAPGVPEWGEGNPELLKTARLWPHRLEGEGHFLARFRKEGGAWSTPRLERPSPLSQEALRAFRGFLEEAGLTLEGPVLDRAGHLYLLPEGLPTLLGLKAPAPGLYLGKVQKGRFLPARALALAFGATLPWPEGLPRLALTPEDPRALAFATGEGVAWEGEDHPLALVVLKTAAGEFPLDFGKAKRGVLRPVGVGLRSH 459
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   |     -       194   |  |204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454     
                                                                                                                                                                                                       178             194 198  |                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                              201

Chain B from PDB  Type:PROTEIN  Length:435
 aligned with RSMF_THET8 | Q5SII2 from UniProtKB/Swiss-Prot  Length:456

    Alignment length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             456   
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454 |   
           RSMF_THET8     5 AFLSRMAELLGEEFPAFLKALTEGKRTYGLRVNTLKLPPEAFQRISPWPLRPIPWCQEGFYYPEEARPGPHPFFYAGLYYIQEPSAQAVGVLLDPKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALAEAFGTYFHRVLLDAPCSGEGMFRKDREAARHWGPSAPKRMAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAHPEFRLEDARLHPLFAPGVPEWGEGNPELLKTARLWPHRLEGEGHFLARFRKEGGAWSTPRLERPSPLSQEALRAFRGFLEEAGLTLEGPVLDRAGHLYLLPEGLPTLLGLKAPAPGLYLGKVQKGRFLPARALALAFGATLPWPEGLPRLALTPEDPRALAFATGEGVAWEGEDHPLALVVLKTAAGEFPLDFGKAKRGVLRPVGVGL---   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.hhhhhhhhhhhh....eeee.....hhhhhhhhh....eee..eeeeee.........hhhhhh..eee..hhhhhhhhhhh.....eeee.....hhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh..eeeeeee.---------------.....-----hhhhhhhhhhhhhh.eeeeeeeeeee...hhhhhhhhhhhhhhhh..eeee........ee.hhhhh..hhhhhh.eee.........eeeeeeee................hhhhhhhhhhhhhhhh..ee..eeee..eeee...........eeee..eeeeeee..eeeehhhhhhhh...........eeee...hhhhhhhhh...ee.....eeeeeeeeee..eeeeeeeeeee..eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_MT_RSMB_NOP  PDB: B:10-300 UniProt: 10-300                                                                                                                                                                                                                                                     --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m6u B   5 AFLSRMAELLGEEFPAFLKALTEGKRTYGLRVNTLKLPPEAFQRISPWPLRPIPWCQEGFYYPEEARPGPHPFFYAGLYYIQEPSAQAVGVLLDPKPGERVLDLAAAPGGKTTHLAARMGGKGLLLANEVDGKRVRGLLENVERWGAPLAVTQAPPRALAEAFGTYFHRVLLDA---------------RHWGP-----MAEVQKALLAQASRLLGPGGVLVYSTCTFAPEENEGVVAHFLKAHPEFRLEDARLHPLFAPGVPEWGEGNPELLKTARLWPHRLEGEGHFLARFRKEGGAWSTPRLERPSPLSQEALRAFRGFLEEAGLTLEGPVLDRAGHLYLLPEGLPTLLGLKAPAPGLYLGKVQKGRFLPARALALAFGATLPWPEGLPRLALTPEDPRALAFATGEGVAWEGEDHPLALVVLKTAAGEFPLDFGKAKRGVLRPVGVGLRSH 459
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174   |     -       194   |   204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454     
                                                                                                                                                                                                       178             194 198   204

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 3M6U)

(no "CATH Domain" information available for 3M6U)

(no "Pfam Domain" information available for 3M6U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RSMF_THET8 | Q5SII2)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	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:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:111 - Pro A:112	[ RasMol ]
		Ala B:111 - Pro B:112	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	RSMF_THET8 \| Q5SII2	:	3m6v 3m6w 3m6x

2frx	E. COLI YEBU
3m6v
3m6w
3m6x

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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