1RL2 - JenaLib

Title :   RIBOSOMAL PROTEIN L2 RNA-BINDING DOMAIN FROM BACILLUS STEAROTHERMOPHILUS

Authors :   A. Nakagawa, H. Hosaka, T. Nakashima, I. Tanaka

Date :   25 Mar 99 (Deposition) - 02 Apr 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Ribosomal Protein, Rna-Binding Domain, Peptidyltransferease Center, X-Ray Diffraction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Nakagawa, T. Nakashima, M. Taniguchi, H. Hosaka, M. Kimura, I. Tanaka
The Three-Dimensional Structure Of The Rna-Binding Domain Of Ribosomal Protein L2; A Protein At The Peptidyl Transferase Center Of The Ribosome.
Embo J. V. 18 1459 1999
PubMed-ID: 10075918 | Reference-DOI: 10.1093/EMBOJ/18.6.1459
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:136
 aligned with RL2_GEOSE | P04257 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:136
                                    70        80        90       100       110       120       130       140       150       160       170       180       190      
            RL2_GEOSE    61 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEVG 196
               SCOP domains d1rl2a2 A:60-125 N-terminal domain of ribosomal protein L2        d1rl2a1 A:126-195 C-terminal domain of ribosomal protein L2            SCOP domains
               CATH domains 1rl2A01 A:60-115 Nucleic acid-binding proteins          -1rl2A02 A:117-195  [code=2.30.30.30, no name defined]                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeehhh.eeeeeeee....eeeee.......................eeehhh............................eeeeee..eeeee.............eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rl2 A  60 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGmEImSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRmILGKCRATVGEVG 195
                                    69        79        89        99       109   |  |119       129       139       149       159       169       179  |    189      
                                                                               113-MSE                                                              182-MSE         
                                                                                  116-MSE

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with RL2_GEOSE | P04257 from UniProtKB/Swiss-Prot  Length:276

    Alignment length:137
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       
            RL2_GEOSE    61 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGMEIMSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRMILGKCRATVGEVGN 197
               SCOP domains d1rl2b2 B:60-125 N-terminal domain of ribosomal protein L2        d1rl2b1 B:126-196 C-terminal domain of ribosomal protein L2             SCOP domains
               CATH domains 1rl2B01 B:60-115 Nucleic acid-binding proteins          -1rl2B02 B:117-192  [code=2.30.30.30, no name defined]                       ---- CATH domains
           Pfam domains (1) Ribosomal_L2-1rl2B03 B:60-117                             -----Ribosomal_L2_C-1rl2B01 B:123-196                                           Pfam domains (1)
           Pfam domains (2) Ribosomal_L2-1rl2B04 B:60-117                             -----Ribosomal_L2_C-1rl2B02 B:123-196                                           Pfam domains (2)
         Sec.struct. author ...............eeeeeeeee....eeeeeeee....eeeee.......................eeehhh............................eeeeee..eeeee.............eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rl2 B  60 QYRIIDFKRDKDGIPGRVATIEYDPNRSANIALINYADGEKRYIIAPKNLKVGmEImSGPDADIKIGNALPLENIPVGTLVHNIELKPGRGGQLVRAAGTSAQVLGKEGKYVIVRLASGEVRmILGKCRATVGEVGN 196
                                    69        79        89        99       109   |  |119       129       139       149       159       169       179  |    189       
                                                                               113-MSE                                                              182-MSE          
                                                                                  116-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 '\|'

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RL2_GEOSE | P04257)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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.
	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: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:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0015934	large ribosomal subunit	The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
	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.

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