T00244
type: Enzyme
cath: http://ezcatdb.cbrc.jp/EzCatDB/cath/-.-.-.-
cath: Ribosomal Protein S5; domain 2
ec: https://purl.uniprot.org/enzyme/3.1.26.5
uniprot: P25814
uniprot: P0A0H5
uniprot: Q9X1H4
kegg enzyme: ribonuclease P
kegg enzyme: RNase P
kegg cofactor: Magnesium
kegg substrate: RNA
kegg substrate: H2O
kegg product: RNA
pdb: 1nbsA
pdb: 1nbsB
pdb: 1a6fA
pdb: 1d6tA
pdb: 1nz0A
pdb: 1nz0B
pdb: 1nz0C
pdb: 1nz0D
pdb bound state: Unbound
  compound: RNA
  pdb: 1a6fA
pdb bound state: Unbound
  compound: RNA
  pdb: 1d6tA
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0A
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0B
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0C
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0D
pdb bound state: Analogue
  compound: Magnesium
  pdb: 1nbsA
  ligand het code: 4x_PB
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1a6fA
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1d6tA
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1nz0A
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1nz0B
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1nz0C
pdb bound state: Unbound
  compound: Magnesium
  pdb: 1nz0D
pdb bound state: Unbound
  compound: RNA
  pdb: 1a6fA
pdb bound state: Unbound
  compound: RNA
  pdb: 1d6tA
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0A
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0B
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0C
pdb bound state: Unbound
  compound: RNA
  pdb: 1nz0D
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 1
  reference section: p.243-246
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 2
  reference section: Fig.7, p.5279-5280
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 3
  reference section: p.10303-10304
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 6
  reference section: Fig.1, p.2426-2427
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 22
reference for catalytic mechanism: ReferenceForCatalyticMechanism
  reference index: 23
  reference section: p.2258-2261
references: Structure and catalytic function in ribonuclease P.
references: Multiple magnesium ions in the ribonuclease P reaction mechanism.
references: A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P.
references: Identification of phosphates involved in catalysis by the ribozyme RNase P RNA.
references: The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept].
references: Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond.
references: Analysis of the functional role of conserved residues in the protein subunit of ribonuclease P from Escherichia coli.
references: Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.
references: Ribonuclease P protein structure: evolutionary origins in the translational apparatus.
references: Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
references: 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.
references: Effects of terminal deletions in C5 protein on promoting RNase P catalysis.
references: 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.
references: Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe.
references: The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.
references: Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
references: Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein.
references: Correlation between processing efficiency for ribonuclease P minimal substrates and conformation of the nucleotide -1 at the cleavage position.
references: Protein cofactor-dependent acquisition of novel catalytic activity by the RNase P ribonucleoprotein of E. coli.
references: Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions.
references: Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
references: 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.
references: Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
references: Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA.
references: Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
references: Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
references: Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.
references: Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P.
references: Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.
references: Crystal structure of the specificity domain of ribonuclease P.
references: High-resolution structure of RNase P protein from Thermotoga maritima.
references: Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
references: Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy.
comment: 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]).

Ribosomal Protein S5; domain 2
type: Cath
references: http://www.cathdb.info/version/latest/superfamily/3.30.230.10

Magnesium
type: KeggCofactor
references: KEGG:C00305
compound type: divalent metal (Ca2+, Mg2+)
references: CHEBI:18420
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

RNA
type: KeggSubstrate
references: KEGG:C00046
compound type: nucleic acids
type: KeggProduct

H2O
type: KeggSubstrate
references: KEGG:C00001
compound type: H2O
references: CHEBI:15377
references: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi

1nz0A
type: Pdb
references: 1nz0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nz0
comment: mutant L41M(selenomethionine)

1nz0B
type: Pdb
references: 1nz0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nz0
comment: mutant L41M(selenomethionine)

1nz0C
type: Pdb
references: 1nz0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nz0
comment: mutant L41M(selenomethionine)

1nz0D
type: Pdb
references: 1nz0
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: PDB:1nz0
comment: mutant L41M(selenomethionine)

Structure and catalytic function in ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/2456878
journal: Cold Spring Harb Symp Quant Biol
volume: 52
pages: 239-48
published year: 1987
authors:
  item: Pace NR
  item: Reich C
  item: James BD
  item: Olsen GJ
  item: Pace B
  item: Waugh DS

Multiple magnesium ions in the ribonuclease P reaction mechanism.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8499432
journal: Biochemistry
volume: 32
pages: 5273-81
published year: 1993
authors:
  item: Smith D
  item: Pace NR

A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7520753
journal: Biochemistry
volume: 33
pages: 10294-304
published year: 1994
authors:
  item: Beebe JA
  item: Fierke CA

Identification of phosphates involved in catalysis by the ribozyme RNase P RNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/7585250
journal: RNA
volume: 1
pages: 210-8
published year: 1995
authors:
  item: Harris ME
  item: Pace NR

The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non-uniformly deuterium labelled counterpart [the 'NMR-window' concept].
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/8668532
journal: Nucleic Acids Res
volume: 24
pages: 2022-35
published year: 1996
authors:
  item: Glemarec C
  item: Kufel J
  item: Foldesi A
  item: Maltseva T
  item: Sandstrom A
  item: Kirsebom LA
  item: Chattopadhyaya J

Ribonuclease P catalysis requires Mg2+ coordinated to the pro-RP oxygen of the scissile bond.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9054547
journal: Biochemistry
volume: 36
pages: 2425-38
published year: 1997
authors:
  item: Chen Y
  item: Li X
  item: Gegenheimer P

Analysis of the functional role of conserved residues in the protein subunit of ribonuclease P from Escherichia coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9135114
journal: J Mol Biol
volume: 267
pages: 818-29
published year: 1997
authors:
  item: Gopalan V
  item: Baxevanis AD
  item: Landsman D
  item: Altman S

Identification by modification-interference of purine N-7 and ribose 2'-OH groups critical for catalysis by bacterial ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9701285
journal: RNA
volume: 4
pages: 937-47
published year: 1998
authors:
  item: Kazantsev AV
  item: Pace NR

Ribonuclease P protein structure: evolutionary origins in the translational apparatus.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
references: http://www.ncbi.nlm.nih.gov/pubmed/9563955
journal: Science
volume: 280
pages: 752-5
published year: 1998
authors:
  item: Stams T
  item: Niranjanakumari S
  item: Fierke CA
  item: Christianson DW
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P25814

Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using electron paramagnetic resonance spectroscopy.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10026248
journal: Biochemistry
volume: 38
pages: 1705-14
published year: 1999
authors:
  item: Gopalan V
  item: Kuhne H
  item: Biswas R
  item: Li H
  item: Brudvig GW
  item: Altman S

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/9889289
journal: Nucleic Acids Res
volume: 27
pages: 895-902
published year: 1999
authors:
  item: Kim S
  item: Sim S
  item: Lee Y

Effects of terminal deletions in C5 protein on promoting RNase P catalysis.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10652223
journal: Biochem Biophys Res Commun
volume: 268
pages: 118-23
published year: 2000
authors:
  item: Kim M
  item: Hyun Park B
  item: Lee Y

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10998249
journal: Biochemistry
volume: 39
pages: 11107-13
published year: 2000
authors:
  item: Fang X
  item: Littrell K
  item: Yang XJ
  item: Henderson SJ
  item: Siefert S
  item: Thiyagarajan P
  item: Pan T
  item: Sosnick TR

Mapping RNA-protein interactions in ribonuclease P from Escherichia coli using disulfide-linked EDTA-Fe.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10656815
journal: J Mol Biol
volume: 296
pages: 19-31
published year: 2000
authors:
  item: Biswas R
  item: Ledman DW
  item: Fox RO
  item: Altman S
  item: Gopalan V

The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA.
type: BibliographicResource
comment: STRUCTURE BY NMR.
references: http://www.ncbi.nlm.nih.gov/pubmed/10623511
journal: J Mol Biol
volume: 295
pages: 105-15
published year: 2000
authors:
  item: Spitzfaden C
  item: Nicholson N
  item: Jones JJ
  item: Guth S
  item: Lehr R
  item: Prescott CD
  item: Hegg LA
  item: Eggleston DS
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: P0A0H5

Solution structure and metal-ion binding of the P4 element from bacterial RNase P RNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/10999599
journal: RNA
volume: 6
pages: 1212-25
published year: 2000
authors:
  item: Schmitz M
  item: Tinoco I Jr

Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11258888
journal: Biochemistry
volume: 40
pages: 2777-89
published year: 2001
authors:
  item: Henkels CH
  item: Kurz JC
  item: Fierke CA
  item: Oas TG

Correlation between processing efficiency for ribonuclease P minimal substrates and conformation of the nucleotide -1 at the cleavage position.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11258957
journal: Biochemistry
volume: 40
pages: 3363-9
published year: 2001
authors:
  item: Zuleeg T
  item: Hansen A
  item: Pfeiffer T
  item: Schubel H
  item: Kreutzer R
  item: Hartmann RK
  item: Limmer S

Protein cofactor-dependent acquisition of novel catalytic activity by the RNase P ribonucleoprotein of E. coli.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11292334
journal: J Mol Biol
volume: 307
pages: 1181-93
published year: 2001
authors:
  item: Cole KB
  item: Dorit RL

Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11266542
journal: Nucleic Acids Res
volume: 29
pages: 1426-32
published year: 2001
authors:
  item: Brannvall M
  item: Mikkelsen NE
  item: Kirsebom LA

Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11328872
journal: Nucleic Acids Res
volume: 29
pages: 1892-7
published year: 2001
authors:
  item: Loria A
  item: Pan T

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.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11926814
journal: Biochemistry
volume: 41
pages: 4533-45
published year: 2002
authors:
  item: Kaye NM
  item: Christian EL
  item: Harris ME

Evidence for a polynuclear metal ion binding site in the catalytic domain of ribonuclease P RNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11980722
journal: EMBO J
volume: 21
pages: 2253-62
published year: 2002
authors:
  item: Christian EL
  item: Kaye NM
  item: Harris ME

Conservation of helical structure contributes to functional metal ion interactions in the catalytic domain of ribonuclease P RNA.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12445779
journal: J Mol Biol
volume: 324
pages: 429-42
published year: 2002
authors:
  item: Kaye NM
  item: Zahler NH
  item: Christian EL
  item: Harris ME

Structure of the UGAGAU hexaloop that braces Bacillus RNase P for action.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/11927952
journal: Nat Struct Biol
volume: 9
pages: 397-403
published year: 2002
authors:
  item: Leeper TC
  item: Martin MB
  item: Kim H
  item: Cox S
  item: Semenchenko V
  item: Schmidt FJ
  item: Van Doren SR

Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12466529
journal: Nucleic Acids Res
volume: 30
pages: 5065-73
published year: 2002
authors:
  item: Jovanovic M
  item: Sanchez R
  item: Altman S
  item: Gopalan V

Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12166648
journal: RNA
volume: 8
pages: 933-47
published year: 2002
authors:
  item: Crary SM
  item: Kurz JC
  item: Fierke CA

Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12831883
journal: Curr Opin Struct Biol
volume: 13
pages: 325-33
published year: 2003
authors:
  item: Harris ME
  item: Christian EL

Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12507471
journal: J Mol Biol
volume: 325
pages: 661-75
published year: 2003
authors:
  item: Tsai HY
  item: Masquida B
  item: Biswas R
  item: Westhof E
  item: Gopalan V

Crystal structure of the specificity domain of ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/12610630
journal: Nature
volume: 421
pages: 760-4
published year: 2003
authors:
  item: Krasilnikov AS
  item: Yang X
  item: Pan T
  item: Mondragon A

High-resolution structure of RNase P protein from Thermotoga maritima.
type: BibliographicResource
comment: X-RAY CRYSTALLOGRAPHY (1.2 A)
references: http://www.ncbi.nlm.nih.gov/pubmed/12799461
journal: Proc Natl Acad Sci U S A
volume: 100
pages: 7497-502
published year: 2003
authors:
  item: Kazantsev AV
  item: Krivenko AA
  item: Harrington DJ
  item: Carter RJ
  item: Holbrook SR
  item: Adams PD
  item: Pace NR
references: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl
references: Q9X1H4

Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/14691942
journal: Biopolymers
volume: 73
pages: 79-89
published year: 2004
authors:
  item: Hsieh J
  item: Andrews AJ
  item: Fierke CA

Change of RNase P RNA function by single base mutation correlates with perturbation of metal ion binding in P4 as determined by NMR spectroscopy.
type: BibliographicResource
references: http://www.ncbi.nlm.nih.gov/pubmed/15576680
journal: Nucleic Acids Res
volume: 32
pages: 6358-66
published year: 2004
authors:
  item: Schmitz M

ReferenceForCatalyticMechanism
reference index: 24
reference section: p.434-439

ReferenceForCatalyticMechanism
reference index: 26

ReferenceForCatalyticMechanism
reference index: 27
reference section: p.936-939, p.942-944

ReferenceForCatalyticMechanism
reference index: 28
reference section: p.329-331

ReferenceForCatalyticMechanism
reference index: 29
reference section: p.672-673