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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROCOCCUS FURIOSUS POP5, AN ARCHAEAL RIBONUCLEASE P PROTEIN
 
Authors :  R. C. Wilson, C. J. Bohlen, M. P. Foster, C. E. Bell
Date :  29 Aug 05  (Deposition) - 24 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Ribonuclease P, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. Wilson, C. J. Bohlen, M. P. Foster, C. E. Bell
Structure Of Pfu Pop5, An Archaeal Rnase P Protein.
Proc. Natl. Acad. Sci. Usa V. 103 873 2006
PubMed-ID: 16418270  |  Reference-DOI: 10.1073/PNAS.0508004103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE P PROTEIN COMPONENT 2
    Chains: A, B, C, D, E
    EC Number: 3.1.26.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-33B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RNP2
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synonym: RNASE P COMPONENT 2

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  B   
Biological Unit 3 (1x):   C  
Biological Unit 4 (1x):    D 
Biological Unit 5 (1x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AV5)

(-) Sites  (0, 0)

(no "Site" information available for 2AV5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2AV5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2AV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AV5)

(-) Exons   (0, 0)

(no "Exon" information available for 2AV5)

(-) 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:106
 aligned with RNP2_PYRFU | Q8U151 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           RNP2_PYRFU    15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRCDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
               SCOP domains d2av5a1 A:15-120 RNase P protein component 2, Rnp2                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2av5 A  15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRSDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain B from PDB  Type:PROTEIN  Length:106
 aligned with RNP2_PYRFU | Q8U151 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           RNP2_PYRFU    15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRCDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
               SCOP domains d2av5b_ B: RNase P protein component 2, Rnp2                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2av5 B  15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRSDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain C from PDB  Type:PROTEIN  Length:106
 aligned with RNP2_PYRFU | Q8U151 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           RNP2_PYRFU    15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRCDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
               SCOP domains d2av5c_ C: RNase P protein component 2, Rnp2                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2av5 C  15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRSDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain D from PDB  Type:PROTEIN  Length:106
 aligned with RNP2_PYRFU | Q8U151 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           RNP2_PYRFU    15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRCDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
               SCOP domains d2av5d_ D: RNase P protein component 2, Rnp2                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2av5 D  15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRSDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain E from PDB  Type:PROTEIN  Length:106
 aligned with RNP2_PYRFU | Q8U151 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           RNP2_PYRFU    15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRCDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
               SCOP domains d2av5e_ E: RNase P protein component 2, Rnp2                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeeee..hhhhhhhhhhh..ee..eeeeeeeeeee.hhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2av5 E  15 KKRYIAFKVISENQFNKDEIKEAIWNACLRTLGELGTAKAKPWLIKFDETTQTGIIRSDRNHVYDVIFSLTLVSDINGNKAIIKVLGVSGTIKRLKRKFLSQFGWR 120
                                    24        34        44        54        64        74        84        94       104       114
   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, 5)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2AV5)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (RNP2_PYRFU | Q8U151)
molecular function
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    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: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.

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