3G88 - JenaLib

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Title :   T. THERMOPHILUS 16S RRNA G527 METHYLTRANSFERASE IN COMPLEX WITH ADOMET IN SPACE GROUP P61

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

Date :   11 Feb 09 (Deposition) - 30 Jun 09 (Release) - 08 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

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

Keywords :   Methyltransferase, 16S Rrna Methyltransferase, Translation, Cytoplasm, Rrna Processing, S-Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. T. Gregory, H. Demirci, R. Belardinelli, T. Monshupanee, C. Gualerzi, A. E. Dahlberg, G. Jogl
Structural And Functional Studies Of The Thermus Thermophilus 16S Rrna Methyltransferase Rsmg
Rna V. 15 1693 2009
PubMed-ID: 19622680 | Reference-DOI: 10.1261/RNA.1652709
(for further references see the PDB file header)

Molecule 1 - RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE G
	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	:	GIDB, RSMG, TTHA1971
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	16S RRNA 7-METHYLGUANOSINE METHYLTRANSFERASE, 16S RRNA M7G METHYLTRANSFERASE, GLUCOSE-INHIBITED DIVISION PROTEIN B

		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 (3, 7)

No.	Name	Count	Type	Full Name
1	HIC	2	Mod. Amino Acid	4-METHYL-HISTIDINE
2	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	HIC	1	Mod. Amino Acid	4-METHYL-HISTIDINE
2	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	HIC	1	Mod. Amino Acid	4-METHYL-HISTIDINE
2	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
3	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:88 , THR A:89 , PHE A:93 , ASP A:111 , ALA A:112 , THR A:113 , GLY A:137 , ARG A:138 , ALA A:139 , GLU A:140 , ARG A:158 , ALA A:159 , HOH A:252 , HOH A:272 , HOH A:282 , HOH A:458 , HOH A:620	BINDING SITE FOR RESIDUE SAM A 303
2	AC2	SOFTWARE	ALA A:112 , TRP A:136 , ARG A:138 , PRO A:196 , HOH A:355 , HOH A:481	BINDING SITE FOR RESIDUE PEG A 250
3	AC3	SOFTWARE	GLY B:88 , THR B:89 , PHE B:93 , ASP B:111 , ALA B:112 , THR B:113 , GLY B:137 , ARG B:138 , ALA B:139 , GLU B:140 , ARG B:158 , ALA B:159 , HOH B:253 , HOH B:264 , HOH B:331 , HOH B:408 , HOH B:437 , HOH B:447	BINDING SITE FOR RESIDUE SAM B 303
4	AC4	SOFTWARE	ALA B:112 , TRP B:136 , GLY B:137 , ARG B:138 , PRO B:196 , HOH B:348 , HOH B:419	BINDING SITE FOR RESIDUE PEG B 250
5	AC5	SOFTWARE	ALA B:91 , LYS B:115 , LYS B:116 , HOH B:613 , HOH B:683 , HOH B:691	BINDING SITE FOR RESIDUE PEG B 251

Asymmetric Unit

No.	Residues
1	A:164	-	A:249
2	B:164	-	B:249

Asymmetric Unit

No.	Residues
1	Phe A:93	-	Pro A:94
2	Tyr A:236	-	Pro A:237
3	Phe B:93	-	Pro B:94
4	Tyr B:236	-	Pro B:237

(no "SAP(SNP)/Variant" information available for 3G88)

(no "PROSITE Motif" information available for 3G88)

(no "Exon" information available for 3G88)

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
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Chain A from PDB  Type:PROTEIN  Length:239
 aligned with RSMG_THET8 | Q9LCY2 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           RSMG_THET8     1 MFHGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g88A00 A:1-249 Vaccinia Virus protein VP39                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh----------hhhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhh........eeeeeee...hhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g88 A   1 MFhGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEA----------GEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
                              |     10        20        30        40     |   -      | 60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
                              |                                         46         57                                                                                                                                                                                                
                              3-HIC

Chain B from PDB  Type:PROTEIN  Length:238
 aligned with RSMG_THET8 | Q9LCY2 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           RSMG_THET8     1 MFHGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEASGKVNLTALRGEEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g88B00 B:1-249 Vaccinia Virus protein VP39                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh-----------hhhhhhhhhhhhhhhhhh.......eeeee......hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhh........eeeeeee...hhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhh.eeeeeeeeee......eeeeeeeee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g88 B   1 MFhGKHPGGLSERGRALLLEGGKALGLDLKPHLEAFSRLYALLQEA-----------EEEVVVKHFLDSLTLLRLPLWQGPLRVLDLGTGAGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHREAYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVLALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPLC 249
                              |     10        20        30        40     |   -       |60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
                              3-HIC                                     46          58

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 3G88)

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. Organism_taxid: 300852. Strain: hb8. (3)

1a	3g88B00	B:1-249
1b	3g88A00	A:1-249

(no "Pfam Domain" information available for 3G88)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RSMG_THET8 | Q9LCY2)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0070043	rRNA (guanine-N7-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N7-methylguanine.
	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:0070476	rRNA (guanine-N7)-methylation	The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an rRNA molecule.
	GO:0031167	rRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an rRNA 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.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:93 - Pro A:94	[ RasMol ]
		Phe B:93 - Pro B:94	[ RasMol ]
		Tyr A:236 - Pro A:237	[ RasMol ]
		Tyr B:236 - Pro B:237	[ RasMol ]

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

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	3g88
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	RSMG_THET8 \| Q9LCY2	:	3g89 3g8a 3g8b

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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