2NXE - JenaLib

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Title :   T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE

Authors :   H. Demirci, S. T. Gregory, A. E. Dahlberg, G. Jogl

Date :   17 Nov 06 (Deposition) - 26 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   S-Adenosyl-L-Methionine Dependent Methyltransferase, Postranslational Modification, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Demirci, S. T. Gregory, A. E. Dahlberg, G. Jogl
Recognition Of Ribosomal Protein L11 By The Protein Trimethyltransferase Prma.
Embo J. V. 26 567 2007
PubMed-ID: 17215866 | Reference-DOI: 10.1038/SJ.EMBOJ.7601508

Molecule 1 - RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30B
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PRMA
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	L11 MTASE

		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	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:99 , GLY A:100 , THR A:107 , ASP A:126 , GLY A:128 , THR A:129 , GLY A:130 , LEU A:134 , ASP A:149 , ILE A:150 , GLY A:174 , SER A:175 , ASN A:191 , LEU A:192 , LEU A:196 , HOH A:306 , HOH A:312 , HOH A:318 , HOH A:336 , HOH A:373 , HOH A:410	BINDING SITE FOR RESIDUE SAM A 302
2	AC2	SOFTWARE	PHE B:99 , GLY B:100 , THR B:107 , ASP B:126 , GLY B:128 , THR B:129 , GLY B:130 , LEU B:134 , ASP B:149 , ILE B:150 , GLY B:174 , SER B:175 , ASN B:191 , LEU B:192 , LEU B:196 , HOH B:308 , HOH B:310 , HOH B:318 , HOH B:325 , HOH B:334 , HOH B:341 , HOH B:395 , HOH B:450	BINDING SITE FOR RESIDUE SAM B 303

(no "SS Bond" information available for 2NXE)

Asymmetric Unit

No.	Residues
1	Pro A:73	-	Pro A:74
2	Gly A:183	-	Pro A:184
3	Pro B:73	-	Pro B:74
4	Gly B:183	-	Pro B:184

(no "SAP(SNP)/Variant" information available for 2NXE)

(no "PROSITE Motif" information available for 2NXE)

(no "Exon" information available for 2NXE)

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:254
 aligned with PRMA_THET8 | Q84BQ9 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
           PRMA_THET8     1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDWLEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
               SCOP domains d2nxea1 A:1-254 PrmA-like protein TTHA0656 (TT0836)                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhh.hhhhhhhh...eeeee..eeeeee..........eeee....hhhhhhhhhh..eee..eeee..........eeee...........hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nxe A   1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDWLEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with PRMA_THET8 | Q84BQ9 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:254
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
           PRMA_THET8     1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVGDEDWLEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
               SCOP domains d2nxeb1 B:1-254 PrmA-like protein TTHA0656 (TT0836)                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------PrmA-2nxeB01 B      :42-254                                                                                                                                                                                           Pfam domains (1)
           Pfam domains (2) -----------------------------------------PrmA-2nxeB02 B      :42-254                                                                                                                                                                                           Pfam domains (2)
         Sec.struct. author .eeeeee.....hhhhhhhhhhh...eeee...eeeeee..........eeee..------hhhhhh..eee..eeee..........eeee...........hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhheeeeeeeeeeeee..hhhhhhhhhhhh..eeeeeeee..eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nxe B   1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEVG------AWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 254
                                    10        20        30        40        50    |    - |      70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    
                                                                                 55     62

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 "CATH Domain" information available for 2NXE)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: PrmA (8)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (7)

1a	PrmA-2nxeB01	B:42-254
1b	PrmA-2nxeB02	B:42-254

Asymmetric Unit(hide GO term definitions)

Chain A,B (PRMA_THET8 | Q84BQ9)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0008276	protein methyltransferase activity	Catalysis of the transfer of a methyl group (CH3-) to a protein.
	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:0006479	protein methylation	The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
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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		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:183 - Pro A:184	[ RasMol ]
		Gly B:183 - Pro B:184	[ RasMol ]
		Pro A:73 - Pro A:74	[ RasMol ]
		Pro B:73 - Pro B:74	[ RasMol ]

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

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	2.1.1.-
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	PRMA_THET8 \| Q84BQ9	:	1ufk 2nxc 2nxj 2nxn 2zbp 2zbq 2zbr 3cjq 3cjr 3cjs 3cjt 3egv

1nxc	T. THERMOPHILUS PRMA AT 1.59A RESOLUTION
1ufk	T. THERMOPHILUS PRMA AT 1.9 A RESOLUTION
2nxj
2nxn

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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