3TQS - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF THE DIMETHYLADENOSINE TRANSFERASE (KSGA) FROM COXIELLA BURNETII

Authors :   M. Rudolph, J. Cheung, M. C. Franklin, M. Cassidy, E. Gary, F. Burshteyn

Date :   09 Sep 11 (Deposition) - 28 Sep 11 (Release) - 10 Feb 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Protein Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Franklin, J. Cheung, M. J. Rudolph, F. Burshteyn, M. Cassidy, E. Gary, B. Hillerich, Z. K. Yao, P. R. Carlier, M. Totrov, J. D. Love
Structural Genomics For Drug Design Against The Pathogen Coxiella Burnetii.
Proteins V. 83 2124 2015
PubMed-ID: 26033498 | Reference-DOI: 10.1002/PROT.24841

Molecule 1 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE A
	Chains	:	A, B, C, D
	EC Number	:	2.1.1.182
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RSMA, KSGA, CBU_1982
	Organism Scientific	:	COXIELLA BURNETII
	Organism Taxid	:	777
	Strain	:	RSA493
	Synonym	:	16S RRNA (ADENINE(1518)-N(6)/ADENINE(1519)-N(6))- DIMETHYLTRANSFERASE, 16S RRNA DIMETHYLADENOSINE TRANSFERASE, 16S RRNA DIMETHYLASE, S-ADENOSYLMETHIONINE-6-N', N'-ADENOSYL(RRNA) DIMETHYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3TQS)

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

Asymmetric Unit

No.	Residues
1	Thr A:175	-	Pro A:176
2	Thr A:194	-	Pro A:195
3	Thr B:175	-	Pro B:176
4	Thr B:194	-	Pro B:195
5	Thr C:175	-	Pro C:176
6	Thr C:194	-	Pro C:195
7	Thr D:175	-	Pro D:176
8	Thr D:194	-	Pro D:195

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_COXBU	36-63	4	A:36-63 B:36-63 C:36-63 D:36-63

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_COXBU	36-63	1	A:36-63 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_COXBU	36-63	1	- B:36-63 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_COXBU	36-63	1	- - C:36-63 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RRNA_A_DIMETH	PS01131	Ribosomal RNA adenine dimethylases signature.	RSMA_COXBU	36-63	1	- - - D:36-63

(no "Exon" information available for 3TQS)

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:247
 aligned with RSMA_COXBU | Q83AC2 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:247
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           RSMA_COXBU    12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDMHFMLQKEVVRRITAEVGSHDYGRLSVMAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
               SCOP domains d3tqsa_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh.....eeeee......hhhhhh....eeeeee.hhhhhhhhhhhhh....eeeee......hhhhh.....eeeeee.hhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: A:36-63 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqs A  12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDmHFmLQKEVVRRITAEVGSHDYGRLSVmAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
                                    21        31        41        51        61        71        81        91       101       111       121       131|      141       151    |  161       171       181       191       201       211       221       231       241       251       
                                                                                                                                               129-MSE                    156-MSE                                                                                                  
                                                                                                                                                  132-MSE

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with RSMA_COXBU | Q83AC2 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:247
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           RSMA_COXBU    12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDMHFMLQKEVVRRITAEVGSHDYGRLSVMAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
               SCOP domains d3tqsb_ B: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh.....eeeee......hhhhhh....eeeeee.hhhhhhhhhhhhh....eeeee......hhhhh.....eeeeee.hhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: B:36-63 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqs B  12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDmHFmLQKEVVRRITAEVGSHDYGRLSVmAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
                                    21        31        41        51        61        71        81        91       101       111       121       131|      141       151    |  161       171       181       191       201       211       221       231       241       251       
                                                                                                                                               129-MSE                    156-MSE                                                                                                  
                                                                                                                                                  132-MSE

Chain C from PDB  Type:PROTEIN  Length:247
 aligned with RSMA_COXBU | Q83AC2 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:247
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           RSMA_COXBU    12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDMHFMLQKEVVRRITAEVGSHDYGRLSVMAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
               SCOP domains d3tqsc_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh.....eeeee......hhhhhh....eeeeee.hhhhhhhhhhhhh....eeeee......hhhhh.....eeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: C:36-63 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqs C  12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDmHFmLQKEVVRRITAEVGSHDYGRLSVmAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
                                    21        31        41        51        61        71        81        91       101       111       121       131|      141       151    |  161       171       181       191       201       211       221       231       241       251       
                                                                                                                                               129-MSE                    156-MSE                                                                                                  
                                                                                                                                                  132-MSE

Chain D from PDB  Type:PROTEIN  Length:247
 aligned with RSMA_COXBU | Q83AC2 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:247
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       
           RSMA_COXBU    12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDMHFMLQKEVVRRITAEVGSHDYGRLSVMAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
               SCOP domains d3tqsd_ D: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhhh.....eeeee......hhhhhh....eeeee..hhhhhhhhhhhhh....eeee.......hhhhh.....eeeeee.hhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhh........hhhhhhhhhheeeeeeeeehhh.ee......eeeeeeee.........hhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------RRNA_A_DIMETH  PDB: D:36-63 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tqs D  12 QHFLHDSFVLQKIVSAIHPQKTDTLVEIGPGRGALTDYLLTECDNLALVEIDRDLVAFLQKKYNQQKNITIYQNDALQFDFSSVKTDKPLRVVGNLPYNISTPLLFHLFSQIHCIEDmHFmLQKEVVRRITAEVGSHDYGRLSVmAQYFCDNTYLFTVSPQAFTPPPRVESAIIRLIPRHNFTPVAKNLDQLSHVVKEAFSYRRKTVGNALKKLINPSQWPLLEINPQLRPQELTVEDFVKISNILN 258
                                    21        31        41        51        61        71        81        91       101       111       121       131|      141       151    |  161       171       181       191       201       211       221       231       241       251       
                                                                                                                                               129-MSE                    156-MSE                                                                                                  
                                                                                                                                                  132-MSE

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)

Coxiella burnetii [TaxId: 777] (2)

1a	d3tqsa_	A:
1b	d3tqsb_	B:
1c	d3tqsc_	C:
1d	d3tqsd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RSMA_COXBU | Q83AC2)

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 3tqs)

	Cis Peptide Bonds
		Thr A:175 - Pro A:176	[ RasMol ]
		Thr A:194 - Pro A:195	[ RasMol ]
		Thr B:175 - Pro B:176	[ RasMol ]
		Thr B:194 - Pro B:195	[ RasMol ]
		Thr C:175 - Pro C:176	[ RasMol ]
		Thr C:194 - Pro C:195	[ RasMol ]
		Thr D:175 - Pro D:176	[ RasMol ]
		Thr D:194 - Pro D:195	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 12)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

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