DB code: S00175

RLCP classification 1.15.60000.85 : Hydrolysis
CATH domain 3.10.450.30 : Nuclear Transport Factor 2; Chain Catalytic domain
E.C. 3.1.27.10
CSA 1de3
M-CSA 1de3
MACiE

CATH domain Related DB codes (homologues)
3.10.450.30 : Nuclear Transport Factor 2; Chain S00174

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P00655 Ribonuclease alpha-sarcin
EC 3.1.27.10
rRNA endonuclease
PF00545 (Ribonuclease)
[Graphical View]

KEGG enzyme name
rRNA endonuclease
alpha-sarcin

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P00655 RNAS_ASPGI Hydrolysis of the phosphodiester linkage between guanosine and adenosine residues at one specific position in 28S rRNA from rat ribosomes. Secreted.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C00240 C00001 C02867
E.C.
Compound rRNA H2O Oligoribonucleotide
Type nucleic acids H2O nucleic acids
ChEBI 15377
PubChem 22247451
962
1de3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1r4yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [1], [2]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1de3A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 50;GLU 96;ARG 121;HIS 137
1r4yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 36;GLU 82;ARG 107;HIS 123

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.7, p.15874 3

References
[1]
Resource
Comments
Medline ID
PubMed ID 9843392
Journal Biochemistry
Year 1998
Volume 37
Pages 15865-76
Authors Perez-Canadillas JM, Campos-Olivas R, Lacadena J, Martinez del Pozo A, Gavilanes JG, Santoro J, Rico M, Bruix M
Title Characterization of pKa values and titration shifts in the cytotoxic ribonuclease alpha-sarcin by NMR. Relationship between electrostatic interactions, structure, and catalytic function.
Related PDB
Related UniProtKB
[2]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10843858
Journal J Mol Biol
Year 2000
Volume 299
Pages 1061-73
Authors Perez-Canadillas JM, Santoro J, Campos-Olivas R, Lacadena J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
Title The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity.
Related PDB 1de3
Related UniProtKB
[3]
Resource
Comments catalysis
Medline ID
PubMed ID 11025546
Journal Proteins
Year 2000
Volume 41
Pages 350-61
Authors de Antonio C, Martinez del Pozo A, Mancheno JM, Onaderra M, Lacadena J, Martinez-Ruiz A, Perez-Canadillas JM, Bruix M, Gavilanes JG
Title Assignment of the contribution of the tryptophan residues to the spectroscopic and functional properties of the ribotoxin alpha-sarcin.
Related PDB
Related UniProtKB
[4]
Resource
Comments catalysis
Medline ID
PubMed ID 11313342
Journal J Biol Chem
Year 2001
Volume 276
Pages 24075-81
Authors Rajamohan F, Mao C, Uckun FM
Title Binding interactions between the active center cleft of recombinant pokeweed antiviral protein and the alpha-sarcin/ricin stem loop of ribosomal RNA.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 12527386
Journal FEBS Lett
Year 2003
Volume 534
Pages 197-201
Authors Perez-Canadilllas JM, Garcia-Mayoral MF, Laurents DV, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
Title Tautomeric state of alpha-sarcin histidines. Ndelta tautomers are a common feature in the active site of extracellular microbial ribonucleases.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 14609322
Journal Biochemistry
Year 2003
Volume 42
Pages 13122-33
Authors Garcia-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
Title Dissecting structural and electrostatic interactions of charged groups in alpha-sarcin. An NMR study of some mutants involving the catalytic residues.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 15044731
Journal Protein Sci
Year 2004
Volume 13
Pages 1000-11
Authors Garcia-Mayoral MF, Garcia-Ortega L, Lillo MP, Santoro J, Martinez del Pozo A, Gavilanes JG, Rico M, Bruix M
Title NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity.
Related PDB 1r4y
Related UniProtKB

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.

Created Updated
2002-07-01 2011-11-01