EzCatDB: T00244
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DB codeT00244
CATH domainDomain 1-.-.-.-
Domain 2-.-.-.-
Domain 33.30.230.10 : Ribosomal Protein S5; domain 2
E.C.3.1.26.5

CATH domainRelated DB codes (homologues)
3.30.230.10 : Ribosomal Protein S5; domain 2M00048,M00213

Enzyme Name
UniProtKBKEGG

P25814P0A0H5Q9X1H4
Protein nameRibonuclease P protein componentRibonuclease P protein componentRibonuclease P protein componentribonuclease P
RNase P
SynonymsRNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
RNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
RNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
RefSeqNP_391985.1 (Protein)
NC_000964.3 (DNA/RNA sequence)

NP_229262.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PfamPF00825 (Ribonuclease_P)
[Graphical view]
PF00825 (Ribonuclease_P)
[Graphical view]
PF00825 (Ribonuclease_P)
[Graphical view]


UniProtKB:Accession NumberP25814P0A0H5Q9X1H4
Entry nameRNPA_BACSURNPA_STAAURNPA_THEMA
ActivityEndonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor.Endonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor.Endonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor.
SubunitConsists of a catalytic RNA component (M1 or rnpB) and a protein subunit.Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit.Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit (By similarity).
Subcellular location


Cofactor



Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00046C00001C00046
CompoundMagnesiumRNAH2ORNA
Typedivalent metal (Ca2+, Mg2+)nucleic acidsH2Onucleic acids
ChEBI18420

15377

PubChem888

962
22247451

            
1nbsAAnalogue:4x_PB   
1nbsBBound:2x_MG,Analogue;2x_PB   
1a6fAUnboundUnbound Unbound
1d6tAUnboundUnbound Unbound
1nz0AUnboundUnbound Unbound
1nz0BUnboundUnbound Unbound
1nz0CUnboundUnbound Unbound
1nz0DUnboundUnbound Unbound

Active-site residues
pdbcomment
         
1nbsA 
1nbsB 
1a6fA 
1d6tA 
1nz0Amutant L41M(selenomethionine)
1nz0Bmutant L41M(selenomethionine)
1nz0Cmutant L41M(selenomethionine)
1nz0Dmutant L41M(selenomethionine)

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.243-246
[2]Fig.7, p.5279-5280
[3]p.10303-10304
[6]Fig.1, p.2426-2427
[22]

[23]p.2258-2261
[24]p.434-439
[26]

[27]p.936-939, p.942-944
[28]p.329-331
[29]p.672-673

references
[1]
PubMed ID2456878
JournalCold Spring Harb Symp Quant Biol
Year1987
Volume52
Pages239-48
AuthorsPace NR, Reich C, James BD, Olsen GJ, Pace B, Waugh DS
TitleStructure and catalytic function in ribonuclease P.
[2]
PubMed ID8499432
JournalBiochemistry
Year1993
Volume32
Pages5273-81
AuthorsSmith D, Pace NR
TitleMultiple magnesium ions in the ribonuclease P reaction mechanism.
[3]
PubMed ID7520753
JournalBiochemistry
Year1994
Volume33
Pages10294-304
AuthorsBeebe JA, Fierke CA
TitleA kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P.
[4]
PubMed ID7585250
JournalRNA
Year1995
Volume1
Pages210-8
AuthorsHarris ME, Pace NR
TitleIdentification of phosphates involved in catalysis by the ribozyme RNase P RNA.
[5]
PubMed ID8668532
JournalNucleic Acids Res
Year1996
Volume24
Pages2022-35
AuthorsGlemarec C, Kufel J, Foldesi A, Maltseva T, Sandstrom A, Kirsebom LA, Chattopadhyaya J
TitleThe NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept].
[6]
PubMed ID9054547
JournalBiochemistry
Year1997
Volume36
Pages2425-38
AuthorsChen Y, Li X, Gegenheimer P
TitleRibonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond.
[7]
PubMed ID9135114
JournalJ Mol Biol
Year1997
Volume267
Pages818-29
AuthorsGopalan V, Baxevanis AD, Landsman D, Altman S
TitleAnalysis of the functional role of conserved residues in the protein subunit of ribonuclease P from Escherichia coli.
[8]
PubMed ID9701285
JournalRNA
Year1998
Volume4
Pages937-47
AuthorsKazantsev AV, Pace NR
TitleIdentification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
PubMed ID9563955
JournalScience
Year1998
Volume280
Pages752-5
AuthorsStams T, Niranjanakumari S, Fierke CA, Christianson DW
TitleRibonuclease P protein structure: evolutionary origins in the translational apparatus.
Related PDB1a6f
Related UniProtKBP25814
[10]
PubMed ID10026248
JournalBiochemistry
Year1999
Volume38
Pages1705-14
AuthorsGopalan V, Kuhne H, Biswas R, Li H, Brudvig GW, Altman S
TitleMapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
[11]
PubMed ID9889289
JournalNucleic Acids Res
Year1999
Volume27
Pages895-902
AuthorsKim S, Sim S, Lee Y
TitleIn vitro analysis of processing at the 3'-end of precursors of M1 RNA, the catalytic subunit of Escherichia coli RNase P: multiple pathways and steps for the processing.
[12]
PubMed ID10652223
JournalBiochem Biophys Res Commun
Year2000
Volume268
Pages118-23
AuthorsKim M, Hyun Park B, Lee Y
TitleEffects of terminal deletions in C5 protein on promoting RNase P catalysis.
[13]
PubMed ID10998249
JournalBiochemistry
Year2000
Volume39
Pages11107-13
AuthorsFang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, Thiyagarajan P, Pan T, Sosnick TR
TitleMg2+-dependent compaction and folding of yeast tRNAPhe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering.
[14]
PubMed ID10656815
JournalJ Mol Biol
Year2000
Volume296
Pages19-31
AuthorsBiswas R, Ledman DW, Fox RO, Altman S, Gopalan V
TitleMapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe.
[15]
CommentsSTRUCTURE BY NMR.
PubMed ID10623511
JournalJ Mol Biol
Year2000
Volume295
Pages105-15
AuthorsSpitzfaden C, Nicholson N, Jones JJ, Guth S, Lehr R, Prescott CD, Hegg LA, Eggleston DS
TitleThe structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.
Related PDB1d6t
Related UniProtKBP0A0H5
[16]
PubMed ID10999599
JournalRNA
Year2000
Volume6
Pages1212-25
AuthorsSchmitz M, Tinoco I Jr
TitleSolution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
[17]
PubMed ID11258888
JournalBiochemistry
Year2001
Volume40
Pages2777-89
AuthorsHenkels CH, Kurz JC, Fierke CA, Oas TG
TitleLinked folding and anion binding of the Bacillus subtilis ribonuclease P protein.
[18]
PubMed ID11258957
JournalBiochemistry
Year2001
Volume40
Pages3363-9
AuthorsZuleeg T, Hansen A, Pfeiffer T, Schubel H, Kreutzer R, Hartmann RK, Limmer S
TitleCorrelation between processing efficiency for ribonuclease P minimal substrates and conformation of the nucleotide -1 at the cleavage position.
[19]
PubMed ID11292334
JournalJ Mol Biol
Year2001
Volume307
Pages1181-93
AuthorsCole KB, Dorit RL
TitleProtein cofactor-dependent acquisition of novel catalytic activity by the RNase P ribonucleoprotein of E. coli.
[20]
PubMed ID11266542
JournalNucleic Acids Res
Year2001
Volume29
Pages1426-32
AuthorsBrannvall M, Mikkelsen NE, Kirsebom LA
TitleMonitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions.
[21]
PubMed ID11328872
JournalNucleic Acids Res
Year2001
Volume29
Pages1892-7
AuthorsLoria A, Pan T
TitleModular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
[22]
PubMed ID11926814
JournalBiochemistry
Year2002
Volume41
Pages4533-45
AuthorsKaye NM, Christian EL, Harris ME
TitleNAIM and site-specific functional group modification analysis of RNase P RNA: magnesium dependent structure within the conserved P1-P4 multihelix junction contributes to catalysis.
[23]
PubMed ID11980722
JournalEMBO J
Year2002
Volume21
Pages2253-62
AuthorsChristian EL, Kaye NM, Harris ME
TitleEvidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
[24]
PubMed ID12445779
JournalJ Mol Biol
Year2002
Volume324
Pages429-42
AuthorsKaye NM, Zahler NH, Christian EL, Harris ME
TitleConservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA.
[25]
PubMed ID11927952
JournalNat Struct Biol
Year2002
Volume9
Pages397-403
AuthorsLeeper TC, Martin MB, Kim H, Cox S, Semenchenko V, Schmidt FJ, Van Doren SR
TitleStructure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
[26]
PubMed ID12466529
JournalNucleic Acids Res
Year2002
Volume30
Pages5065-73
AuthorsJovanovic M, Sanchez R, Altman S, Gopalan V
TitleElucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
[27]
PubMed ID12166648
JournalRNA
Year2002
Volume8
Pages933-47
AuthorsCrary SM, Kurz JC, Fierke CA
TitleSpecific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.
[28]
PubMed ID12831883
JournalCurr Opin Struct Biol
Year2003
Volume13
Pages325-33
AuthorsHarris ME, Christian EL
TitleRecent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P.
[29]
PubMed ID12507471
JournalJ Mol Biol
Year2003
Volume325
Pages661-75
AuthorsTsai HY, Masquida B, Biswas R, Westhof E, Gopalan V
TitleMolecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.
[30]
PubMed ID12610630
JournalNature
Year2003
Volume421
Pages760-4
AuthorsKrasilnikov AS, Yang X, Pan T, Mondragon A
TitleCrystal structure of the specificity domain of ribonuclease P.
[31]
CommentsX-RAY CRYSTALLOGRAPHY (1.2 A)
PubMed ID12799461
JournalProc Natl Acad Sci U S A
Year2003
Volume100
Pages7497-502
AuthorsKazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR
TitleHigh-resolution structure of RNase P protein from Thermotoga maritima.
Related PDB1nz0
Related UniProtKBQ9X1H4
[32]
PubMed ID14691942
JournalBiopolymers
Year2004
Volume73
Pages79-89
AuthorsHsieh J, Andrews AJ, Fierke CA
TitleRoles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
[33]
PubMed ID15576680
JournalNucleic Acids Res
Year2004
Volume32
Pages6358-66
AuthorsSchmitz M
TitleChange of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy.

comments
This enzyme is a ribozyme, which is composed of two RNA components (a catalytic component and a specificity domain), and a protein subunit. "Protein C5" is another synonym of the protein subunit.
The tertiary structures of the catalytic doman of the RNA component has not been solved yet, whereas the structures of the specificity domain (PDB;1nbs, 1nxl) have been elucidated (see [30]).

createdupdated
2005-04-152009-03-10


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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