EzCatDB: S00175
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DB codeS00175
RLCP classification1.15.60000.85 : Hydrolysis
CATH domainDomain 13.10.450.30 : Nuclear Transport Factor 2; ChainCatalytic domain
E.C.3.1.27.10
CSA1de3

CATH domainRelated DB codes (homologues)
3.10.450.30 : Nuclear Transport Factor 2; ChainS00174

Enzyme Name
UniProtKBKEGG

P00655
Protein nameRibonuclease alpha-sarcinrRNA endonuclease
alpha-sarcin
SynonymsEC 3.1.27.10
rRNA endonuclease
PfamPF00545 (Ribonuclease)
[Graphical view]


UniProtKB:Accession NumberP00655
Entry nameRNAS_ASPGI
ActivityHydrolysis of the phosphodiester linkage between guanosine and adenosine residues at one specific position in 28S rRNA from rat ribosomes.
Subunit
Subcellular locationSecreted.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00240C00001C02867
CompoundrRNAH2OOligoribonucleotide
Typenucleic acidsH2Onucleic acids
ChEBI
15377

PubChem
962
22247451

           
1de3AUnboundUnboundUnbound
1r4yAUnboundUnboundUnbound

Active-site residues
resource
literature [1], [2]
pdbCatalytic residues
         
1de3AHIS 50;GLU 96;ARG 121;HIS 137
1r4yAHIS 36;GLU 82;ARG 107;HIS 123

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]Fig.7, p.158743

references
[1]
PubMed ID9843392
JournalBiochemistry
Year1998
Volume37
Pages15865-76
AuthorsPerez-Canadillas JM, Campos-Olivas R, Lacadena J, Martinez del Pozo A, Gavilanes JG, Santoro J, Rico M, Bruix M
TitleCharacterization of pKa values and titration shifts in the cytotoxic ribonuclease alpha-sarcin by NMR. Relationship between electrostatic interactions, structure, and catalytic function.
[2]
CommentsX-ray crystallography
PubMed ID10843858
JournalJ Mol Biol
Year2000
Volume299
Pages1061-73
AuthorsPerez-Canadillas JM, Santoro J, Campos-Olivas R, Lacadena J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
TitleThe highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity.
Related PDB1de3
[3]
Commentscatalysis
PubMed ID11025546
JournalProteins
Year2000
Volume41
Pages350-61
Authorsde Antonio C, Martinez del Pozo A, Mancheno JM, Onaderra M, Lacadena J, Martinez-Ruiz A, Perez-Canadillas JM, Bruix M, Gavilanes JG
TitleAssignment of the contribution of the tryptophan residues to the spectroscopic and functional properties of the ribotoxin alpha-sarcin.
[4]
Commentscatalysis
PubMed ID11313342
JournalJ Biol Chem
Year2001
Volume276
Pages24075-81
AuthorsRajamohan F, Mao C, Uckun FM
TitleBinding interactions between the active center cleft of recombinant pokeweed antiviral protein and the alpha-sarcin/ricin stem loop of ribosomal RNA.
[5]
PubMed ID12527386
JournalFEBS Lett
Year2003
Volume534
Pages197-201
AuthorsPerez-Canadilllas JM, Garcia-Mayoral MF, Laurents DV, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
TitleTautomeric state of alpha-sarcin histidines. Ndelta tautomers are a common feature in the active site of extracellular microbial ribonucleases.
[6]
PubMed ID14609322
JournalBiochemistry
Year2003
Volume42
Pages13122-33
AuthorsGarcia-Mayoral MF, Perez-Canadillas JM, Santoro J, Ibarra-Molero B, Sanchez-Ruiz JM, Lacadena J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
TitleDissecting structural and electrostatic interactions of charged groups in alpha-sarcin. An NMR study of some mutants involving the catalytic residues.
[7]
PubMed ID15044731
JournalProtein Sci
Year2004
Volume13
Pages1000-11
AuthorsGarcia-Mayoral MF, Garcia-Ortega L, Lillo MP, Santoro J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
TitleNMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity.
Related PDB1r4y

comments
Glu96 and His137 (of 1de3) acts as a general base and general acid, respectively [1]. The transphosphorylation and hydrolysis steps of the reaction follow a concerted in-line mechanism, implying residues acting as a base and an acid located on either side of the scissile bond. Structurally, Glu96 and His137 are on opposite sides of the active center and have the correct geometry for the in-line cleavage of the dinucleotide.
According to the literature [1] & [6], the reaction proceeds as follows:
(1) Glu96 exists predominantly in the ionized state and acts as a general base abstracting a proton from the 2'-OH group in the ribose ring of the nucleotide.
(2) The activated 2'-hydroxy oxygen makes a nucleophilic attack on the scissile phosphorus atom.
(3) Arg121 is involved in catalysis, probably as a stabilizer for the negative charge on the phosphoryl group.
(4) Meanwhile, His137 remains protonated to serve as general acid and acts as a proton donor to the leaving O5' ester oxygen.
(5) 2',3'-cyclic intermediate is formed.
(6) Glu96 and His137 act as a general acid and base, respectively. Glu96 activates a water molecule, which attacks on the cyclic intermediate, whereas His137 protonates the leaving 2'-oxygen.

createdupdated
2002-07-012011-11-01


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