1PC0 - JenaLib

Title :   NMR STRUCTURE OF THE ARCHAEAL HOMOLOGUE OF RNASE P PROTEIN RPP29

Authors :   D. J. Sidote, D. W. Hoffman

Date :   15 May 03 (Deposition) - 09 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (10x)

Keywords :   Sandwich, Beta-Sheet, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Sidote, D. W. Hoffman
Nmr Structure Of An Archaeal Homologue Of Ribonuclease P Protein Rpp29
Biochemistry V. 42 13541 2003
PubMed-ID: 14622001 | Reference-DOI: 10.1021/BI030170Z
(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 (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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:61
 aligned with RNP1_ARCFU | O28362 from UniProtKB/Swiss-Prot  Length:102

    Alignment length:61
                                    26        36        46        56        66        76 
            RNP1_ARCFU   17 GLMVEVVESPNHSEVGIKGEVVDETQNTLKIMTEKGLKVVAKRGRTFRVWYKGKIMRIKGD 77
               SCOP domains d1pc0a_ A: Hypothetical protein AF1917                        SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeeeeee......eeee....eeee.....eeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  1pc0 A 17 GLMVEVVESPNHSEVGIKGEVVDETQNTLKIMTEKGLKVVAKRGRTFRVWYKGKIMRIKGD 77
                                    26        36        46        56        66        76

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

NMR Structure(hide GO term definitions)

Chain A (RNP1_ARCFU | O28362)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0004526	ribonuclease P activity	Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	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:0006379	mRNA cleavage	Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000172	ribonuclease MRP complex	A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication.
	GO:0030677	ribonuclease P complex	A ribonucleoprotein complex that catalyzes cleavage of the leader sequence of precursor tRNAs (pre-tRNAs), generating the mature 5' end of tRNAs.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1pc0)

	Sites
(no "Sites" information available for 1pc0)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pc0)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1pc0
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNP1_ARCFU \| O28362
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RNP1_ARCFU \| O28362
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description