2CZW - JenaLib

Title :   CRYSTAL STRUCTURE ANALYSIS OF PROTEIN COMPONENT PH1496P OF P.HORIKOSHII RIBONUCLEASE P

Authors :   H. Fukuhara, M. Kifusa, M. Watanabe, A. Terada, T. Honda, T. Numata, Y. Kakuta, M. Kimura

Date :   19 Jul 05 (Deposition) - 25 Apr 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Ribonuclease P, Ribonucleoprotein, Ribosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Fukuhara, M. Kifusa, M. Watanabe, A. Terada, T. Honda, T. Numata, Y. Kakuta, M. Kimura
A Fifth Protein Subunit Ph1496P Elevates The Optimum Temperature For The Ribonuclease P Activity From Pyrococcus Horikoshii Ot3
Biochem. Biophys. Res. Commun. V. 343 956 2006
PubMed-ID: 16574071 | Reference-DOI: 10.1016/J.BBRC.2006.02.192
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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)
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Chain A from PDB  Type:PROTEIN  Length:118
 aligned with RL7A_PYRHO | P62009 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:118
                                    15        25        35        45        55        65        75        85        95       105       115        
           RL7A_PYRHO     6 YVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVRELMK 123
               SCOP domains d2czwa1 A:7-124 Ribosomal protein L7ae                                                                                 SCOP domains
               CATH domains 2czwA00 A:7-124  [code=3.30.1330.30, no name defined]                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhheeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhhh..eeee.hhhhhhhhhh......eeeeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------RIBOSOMAL_L7AE    ------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2czw A   7 YVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVRELMK 124
                                    16        26        36        46        56        66        76        86        96       106       116

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RL7A_PYRHO | P62009)

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:0004526	ribonuclease P activity	Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	GO:0001682	tRNA 5'-leader removal	Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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: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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	Cis Peptide Bonds
		Asp A:59 - Pro A:60	[ RasMol ]

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