3FUT - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P21212

Authors :   H. Demirci, R. Belardinelli, E. Seri, S. T. Gregory, C. Gualerzi, A. E. D G. Jogl

Date :   14 Jan 09 (Deposition) - 31 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.52

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

Keywords :   Methyltransferase, Dimethyltransferase, Dual-Specific Methyltransferase, 16S Rrna Methyltransferase, Translation, Antibiotic Resistance, Rna-Binding, Rrna Processing, S-Adenosyl-L- Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Demirci, R. Belardinelli, E. Seri, S. T. Gregory, C. Gualerzi, A. E. Dahlberg, G. Jogl
Structural Rearrangements In The Active Site Of The Thermus Thermophilus 16S Rrna Methyltransferase Ksga In A Binary Complex With 5'-Methylthioadenosine.
J. Mol. Biol. V. 388 271 2009
PubMed-ID: 19285505 | Reference-DOI: 10.1016/J.JMB.2009.02.066

Molecule 1 - DIMETHYLADENOSINE TRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET26B
	Expression System Strain	:	BL21 (DE3)STAR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KSGA, TTHA0083
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLASE, HIGH LEVEL KASUGAMYCIN RESISTANCE PROTEIN KSGA, KASUGAMYCIN DIMETHYLTRANSFERASE

		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, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3FUT)

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

Asymmetric Unit

No.	Residues
1	Arg A:44	-	Pro A:45
2	Phe A:185	-	Pro A:186
3	Arg B:44	-	Pro B:45
4	Phe B:185	-	Pro B:186

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_RNA_A_N6_MT	PS51689	rRNA adenine N(6)-methyltransferase family profile.	RSMA_THET8	21-271	2	A:21-268 B:25-268
2	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_THET8	50-77	2	A:50-77 B:50-77

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_RNA_A_N6_MT	PS51689	rRNA adenine N(6)-methyltransferase family profile.	RSMA_THET8	21-271	1	A:21-268 -
2	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_THET8	50-77	1	A:50-77 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAM_RNA_A_N6_MT	PS51689	rRNA adenine N(6)-methyltransferase family profile.	RSMA_THET8	21-271	1	- B:25-268
2	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_THET8	50-77	1	- B:50-77

(no "Exon" information available for 3FUT)

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:264
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:264
                                    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    
           RSMA_THET8     5 ASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3futa_ A: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3futA01 A:5-203 Vaccinia Virus protein VP39                                                                                                                                                            ----------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...........ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh.....eeee.hhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhh.....hhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------SAM_RNA_A_N6_MT  PDB: A:21-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) ---------------------------------------------RRNA_A_DIMETH  PDB: A:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fut A   5 ASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERmTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    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    
                                                                                                                                                                            151-MSE

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with RSMA_THET8 | Q5SM60 from UniProtKB/Swiss-Prot  Length:271

    Alignment length:266
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
           RSMA_THET8     3 KLASPQSVRALLERHGLFADKRFGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLPYHIATPLVTRLLKTGRFARLVFLVQKEVAERMTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
               SCOP domains d3futb_ B: automat    ed matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3futB01 B:3-203 Va    ccinia Virus protein VP39                                                                                                                                                          ----------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...----....ee.hhhhhhhhhhhhh.....eeee....hhhhhhhhhh...eeeee.hhhhhhhhhhhh....eeeee.hhhhhhhhhh...eeeeeee.--hhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.....hhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------SAM_RNA_A_N6_MT  PDB: B:25-268 UniProt: 21-271                                                                                                                                                                                                           PROSITE (1)
                PROSITE (2) -----------------------------------------------RRNA_A_DIMETH  PDB: B:50-77 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fut B   3 KLASPQSVRALLERHGLF----FGQNFLVSEAHLRRIVEAARPFTGPVFEVGPGLGALTRALLEAGAEVTAIEKDLRLRPVLEETLSGLPVRLVFQDALLYPWEEVPQGSLLVANLP--IATPLVTRLLKTGRFARLVFLVQKEVAERmTARPKTPAYGVLTLRVAHHAVAERLFDLPPGAFFPPPKVWSSLVRLTPTGALDDPGLFRLVEAAFGKRRKTLLNALAAAGYPKARVEEALRALGLPPRVRAEELDLEAFRRLREGLE 268
                                    12       | -  |     32        42        52        62        72        82        92       102       112      |122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
                                            20   25                                                                                           119  |                          151-MSE                                                                                                                 
                                                                                                                                                 122

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: automated matches (94)

Protein domain: automated matches (94)

Thermus thermophilus HB8 [TaxId: 300852] (5)

1a	d3futa_	A:
1b	d3futb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. (7)

1a	3futA01	A:5-203
1b	3futB01	B:3-203

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (RSMA_THET8 | Q5SM60)

molecular function
	GO:0052908	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity	Catalysis of the reaction: 4 S-adenosyl-L-methionine + adenine(1518)/adenine(1519) in 16S rRNA = 4 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(1518)/N(6)-dimethyladenine(1519) in 16S rRNA.
	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:0016433	rRNA (adenine) methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyladenine.
	GO:0000179	rRNA (adenine-N6,N6-)-dimethyltransferase activity	Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor.
	GO:0008649	rRNA methyltransferase activity	Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA 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:0031167	rRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
	GO:0000154	rRNA modification	The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically.
	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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	Sites
(no "Sites" information available for 3fut)

	Cis Peptide Bonds
		Arg A:44 - Pro A:45	[ RasMol ]
		Arg B:44 - Pro B:45	[ RasMol ]
		Phe A:185 - Pro A:186	[ RasMol ]
		Phe B:185 - Pro B:186	[ RasMol ]

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

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	3fut
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	2.1.1.-
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UniProtKB/Swiss-Prot
	RSMA_THET8 \| Q5SM60	:	3fuu 3fuv 3fuw 3fux

3fuu	T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH ADENOSINE IN SPACE GROUP P212121
3fuv	APO-FORM OF T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN SPACE GROUP P43212
3fuw	T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121
3fux	T. THERMOPHILUS 16S RRNA A1518 AND A1519 METHYLTRANSFERASE (KSGA) IN COMPLEX WITH 5'-METHYLTHIOADENOSINE IN SPACE GROUP P212121

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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