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Title :   RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH RIBOSOMAL PROTEIN L11 (K39A) AND INHIBITOR SINEFUNGIN.

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

Date :   13 Mar 08 (Deposition) - 20 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym./Biol. Unit : A,B

Keywords :   S-Adenosyl-L-Methionine Dependent Methyltransferase, Post- Translational Modification, Multi-Specific Trimethylation, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna-Binding, Transferase-Ribosomal Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Demirci, S. T. Gregory, A. E. Dahlberg, G. Jogl
Multiple-Site Trimethylation Of Ribosomal Protein L11 By Th Prma Methyltransferase.
Structure V. 16 1059 2008
PubMed-ID: 18611379 | Reference-DOI: 10.1016/J.STR.2008.03.016

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

Molecule 2 - 50S RIBOSOMAL PROTEIN L11
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Vector Type	:	PLASMID
	Gene	:	RPLK, RPL11
	Mutation	:	YES
	Organism Scientific	:	THERMUS THERMOPHILUS
	Strain	:	HB8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SFG	1	Ligand/Ion	SINEFUNGIN

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:99 , GLY A:100 , THR A:107 , GLY A:128 , THR A:129 , LEU A:134 , ASP A:149 , ILE A:150 , GLY A:174 , SER A:175 , ASN A:191 , LEU A:192 , HOH A:285 , HOH A:286 , HOH A:314 , HOH A:375 , HOH A:469 , HOH A:473 , HOH A:497	BINDING SITE FOR RESIDUE SFG A 255

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:73	-	Pro A:74
2	Gly A:183	-	Pro A:184
3	Met B:1	-	Lys B:2
4	Pro B:21	-	Pro B:22
5	Thr B:71	-	Pro B:72
6	Met B:134	-	Gly B:135

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_THETH	125-140	1	B:125-137

(no "Exon" information available for 3CJR)

Asymmetric/Biological 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:249
 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 d3cjra1 A:1-254 PrmA-like protein TTHA0656 (TT0836)                                                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhh..eeee...eeeeee..........eee..-----hhhhhhh...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
                 3cjr A   1 MWVYRLKGTLEALDPILPGLFDGGARGLWEREGEVWAFFPAPVDLPYEGVWEEV-----LEAWRRDLKPALAPPFVVLAPWHTWEGAEIPLVIEPGMAFGTGHHETTRLALKALARHLRPGDKVLDLGTGSGVLAIAAEKLGGKALGVDIDPMVLPQAEANAKRNGVRPRFLEGSLEAALPFGPFDLLVANLYAELHAALAPRYREALVPGGRALLTGILKDRAPLVREAMAGAGFRPLEEAAEGEWVLLAYGR 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    
                                                                                54    60

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with RL11_THETH | P36238 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       
           RL11_THETH     1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVE 137
               SCOP domains d3cjrb2 B:1-70 Ribosomal protein L11, N-terminal domain               d3cjrb1 B                   :71-137 Ribosomal protein L11, C-termin SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeee........hhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeee....eeeee...hhhhhhh-------------------...hhhhhhhhhh...........hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------RIBOSOMAL_L11 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cjr B   1 MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVAAFNAATANMGDAIVPVEITIYADRSFTFVTKTPPASYLIR-------------------ITWEQVLEIAKQKMPDLNTTDLEAAARMIAGSARSMGVE 137
                                    10        20        30        40        50        60        70        |-         -       100       110       120       130       
                                                                                                         79                  99

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 3CJR)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain B (RL11_THETH | P36238)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0070180	large ribosomal subunit rRNA binding	Interacting selectively and non-covalently with the large ribosomal subunit RNA (LSU rRNA), a constituent of the large ribosomal subunit. In S. cerevisiae, this is the 25S rRNA.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:183 - Pro A:184	[ RasMol ]
		Met B:1 - Lys B:2	[ RasMol ]
		Met B:134 - Gly B:135	[ RasMol ]
		Pro A:73 - Pro A:74	[ RasMol ]
		Pro B:21 - Pro B:22	[ RasMol ]
		Thr B:71 - Pro B:72	[ RasMol ]

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1ufk	APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA)AT 1.9 A RESOLUTION
2nxc	APO-FORM OF T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA)AT 1.59 A RESOLUTION
2nxe	T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH S-ADENOSYL-L-METHIONINE
2nxj	T.THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN SPACE GROUP P 21 21 2
2nxn	T. THERMOPHILUS RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH RIBOSOMAL PROTEIN L11
3cjq	RIBOSOMAL PROTEIN L11 METHYLTRANSFERASE (PRMA) IN COMPLEX WITH DIMETHYLATED RIBOSOMAL PROTEIN L11 IN SPACE GROUP P212121
3cjs
3cjt
3cju

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

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