DB code: T00244

CATH domain -.-.-.- :
-.-.-.- :
3.30.230.10 : Ribosomal Protein S5; domain 2
E.C. 3.1.26.5
CSA
M-CSA
MACiE

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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P25814 Ribonuclease P protein component
RNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
NP_391985.1 (Protein)
NC_000964.3 (DNA/RNA sequence)
PF00825 (Ribonuclease_P)
[Graphical View]
P0A0H5 Ribonuclease P protein component
RNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
PF00825 (Ribonuclease_P)
[Graphical View]
Q9X1H4 Ribonuclease P protein component
RNaseP protein
RNase P protein
EC 3.1.26.5
Protein C5
NP_229262.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PF00825 (Ribonuclease_P)
[Graphical View]

KEGG enzyme name
ribonuclease P
RNase P

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P25814 RNPA_BACSU Endonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit.
P0A0H5 RNPA_STAAU Endonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit.
Q9X1H4 RNPA_THEMA Endonucleolytic cleavage of RNA, removing 5''- extranucleotides from tRNA precursor. Consists of a catalytic RNA component (M1 or rnpB) and a protein subunit (By similarity).

KEGG Pathways
Map code Pathways E.C.

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00046 C00001 C00046
E.C.
Compound Magnesium RNA H2O RNA
Type divalent metal (Ca2+, Mg2+) nucleic acids H2O nucleic acids
ChEBI 18420
15377
PubChem 888
22247451
962
1nbsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:4x_PB
1nbsB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG,Analogue;2x_PB
1a6fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1d6tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nz0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nz0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nz0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1nz0D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1nbsA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nbsB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1a6fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1d6tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1nz0A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant L41M(selenomethionine)
1nz0B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant L41M(selenomethionine)
1nz0C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant L41M(selenomethionine)
1nz0D Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain mutant L41M(selenomethionine)

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 2456878
Journal Cold Spring Harb Symp Quant Biol
Year 1987
Volume 52
Pages 239-48
Authors Pace NR, Reich C, James BD, Olsen GJ, Pace B, Waugh DS
Title Structure and catalytic function in ribonuclease P.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8499432
Journal Biochemistry
Year 1993
Volume 32
Pages 5273-81
Authors Smith D, Pace NR
Title Multiple magnesium ions in the ribonuclease P reaction mechanism.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7520753
Journal Biochemistry
Year 1994
Volume 33
Pages 10294-304
Authors Beebe JA, Fierke CA
Title A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7585250
Journal RNA
Year 1995
Volume 1
Pages 210-8
Authors Harris ME, Pace NR
Title Identification of phosphates involved in catalysis by the ribozyme RNase P RNA.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8668532
Journal Nucleic Acids Res
Year 1996
Volume 24
Pages 2022-35
Authors Glemarec C, Kufel J, Foldesi A, Maltseva T, Sandstrom A, Kirsebom LA, Chattopadhyaya J
Title The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept].
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9054547
Journal Biochemistry
Year 1997
Volume 36
Pages 2425-38
Authors Chen Y, Li X, Gegenheimer P
Title Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9135114
Journal J Mol Biol
Year 1997
Volume 267
Pages 818-29
Authors Gopalan V, Baxevanis AD, Landsman D, Altman S
Title Analysis of the functional role of conserved residues in the protein subunit of ribonuclease P from Escherichia coli.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9701285
Journal RNA
Year 1998
Volume 4
Pages 937-47
Authors Kazantsev AV, Pace NR
Title Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID
PubMed ID 9563955
Journal Science
Year 1998
Volume 280
Pages 752-5
Authors Stams T, Niranjanakumari S, Fierke CA, Christianson DW
Title Ribonuclease P protein structure: evolutionary origins in the translational apparatus.
Related PDB 1a6f
Related UniProtKB P25814
[10]
Resource
Comments
Medline ID
PubMed ID 10026248
Journal Biochemistry
Year 1999
Volume 38
Pages 1705-14
Authors Gopalan V, Kuhne H, Biswas R, Li H, Brudvig GW, Altman S
Title Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9889289
Journal Nucleic Acids Res
Year 1999
Volume 27
Pages 895-902
Authors Kim S, Sim S, Lee Y
Title In 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.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 10652223
Journal Biochem Biophys Res Commun
Year 2000
Volume 268
Pages 118-23
Authors Kim M, Hyun Park B, Lee Y
Title Effects of terminal deletions in C5 protein on promoting RNase P catalysis.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 10998249
Journal Biochemistry
Year 2000
Volume 39
Pages 11107-13
Authors Fang X, Littrell K, Yang XJ, Henderson SJ, Siefert S, Thiyagarajan P, Pan T, Sosnick TR
Title Mg2+-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.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 10656815
Journal J Mol Biol
Year 2000
Volume 296
Pages 19-31
Authors Biswas R, Ledman DW, Fox RO, Altman S, Gopalan V
Title Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe.
Related PDB
Related UniProtKB
[15]
Resource
Comments STRUCTURE BY NMR.
Medline ID
PubMed ID 10623511
Journal J Mol Biol
Year 2000
Volume 295
Pages 105-15
Authors Spitzfaden C, Nicholson N, Jones JJ, Guth S, Lehr R, Prescott CD, Hegg LA, Eggleston DS
Title The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.
Related PDB 1d6t
Related UniProtKB P0A0H5
[16]
Resource
Comments
Medline ID
PubMed ID 10999599
Journal RNA
Year 2000
Volume 6
Pages 1212-25
Authors Schmitz M, Tinoco I Jr
Title Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11258888
Journal Biochemistry
Year 2001
Volume 40
Pages 2777-89
Authors Henkels CH, Kurz JC, Fierke CA, Oas TG
Title Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11258957
Journal Biochemistry
Year 2001
Volume 40
Pages 3363-9
Authors Zuleeg T, Hansen A, Pfeiffer T, Schubel H, Kreutzer R, Hartmann RK, Limmer S
Title Correlation between processing efficiency for ribonuclease P minimal substrates and conformation of the nucleotide -1 at the cleavage position.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11292334
Journal J Mol Biol
Year 2001
Volume 307
Pages 1181-93
Authors Cole KB, Dorit RL
Title Protein cofactor-dependent acquisition of novel catalytic activity by the RNase P ribonucleoprotein of E. coli.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11266542
Journal Nucleic Acids Res
Year 2001
Volume 29
Pages 1426-32
Authors Brannvall M, Mikkelsen NE, Kirsebom LA
Title Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11328872
Journal Nucleic Acids Res
Year 2001
Volume 29
Pages 1892-7
Authors Loria A, Pan T
Title Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 11926814
Journal Biochemistry
Year 2002
Volume 41
Pages 4533-45
Authors Kaye NM, Christian EL, Harris ME
Title NAIM and site-specific functional group modification analysis of RNase P RNA: magnesium dependent structure within the conserved P1-P4 multihelix junction contributes to catalysis.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 11980722
Journal EMBO J
Year 2002
Volume 21
Pages 2253-62
Authors Christian EL, Kaye NM, Harris ME
Title Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12445779
Journal J Mol Biol
Year 2002
Volume 324
Pages 429-42
Authors Kaye NM, Zahler NH, Christian EL, Harris ME
Title Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11927952
Journal Nat Struct Biol
Year 2002
Volume 9
Pages 397-403
Authors Leeper TC, Martin MB, Kim H, Cox S, Semenchenko V, Schmidt FJ, Van Doren SR
Title Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 12466529
Journal Nucleic Acids Res
Year 2002
Volume 30
Pages 5065-73
Authors Jovanovic M, Sanchez R, Altman S, Gopalan V
Title Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 12166648
Journal RNA
Year 2002
Volume 8
Pages 933-47
Authors Crary SM, Kurz JC, Fierke CA
Title Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12831883
Journal Curr Opin Struct Biol
Year 2003
Volume 13
Pages 325-33
Authors Harris ME, Christian EL
Title Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 12507471
Journal J Mol Biol
Year 2003
Volume 325
Pages 661-75
Authors Tsai HY, Masquida B, Biswas R, Westhof E, Gopalan V
Title Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 12610630
Journal Nature
Year 2003
Volume 421
Pages 760-4
Authors Krasilnikov AS, Yang X, Pan T, Mondragon A
Title Crystal structure of the specificity domain of ribonuclease P.
Related PDB
Related UniProtKB
[31]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.2 A)
Medline ID
PubMed ID 12799461
Journal Proc Natl Acad Sci U S A
Year 2003
Volume 100
Pages 7497-502
Authors Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR
Title High-resolution structure of RNase P protein from Thermotoga maritima.
Related PDB 1nz0
Related UniProtKB Q9X1H4
[32]
Resource
Comments
Medline ID
PubMed ID 14691942
Journal Biopolymers
Year 2004
Volume 73
Pages 79-89
Authors Hsieh J, Andrews AJ, Fierke CA
Title Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
Related PDB
Related UniProtKB
[33]
Resource
Comments
Medline ID
PubMed ID 15576680
Journal Nucleic Acids Res
Year 2004
Volume 32
Pages 6358-66
Authors Schmitz M
Title Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy.
Related PDB
Related UniProtKB

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]).

Created Updated
2005-04-15 2009-03-10