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PDBsum entry 2aad
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protein ligands metals Protein-protein interface(s) links
Hydrolase(endoribonuclease) PDB id
2aad

 

 

 

 

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Contents
Protein chains
104 a.a. *
Ligands
2GP ×2
Metals
_CA ×2
Waters ×239
* Residue conservation analysis
PDB id:
2aad
Name: Hydrolase(endoribonuclease)
Title: The role of histidine-40 in ribonuclease t1 catalysis: three- dimensional structures of the partially active his40lys mutant
Structure: Ribonuclease t1 isozyme. Chain: a, b. Engineered: yes
Source: Aspergillus oryzae. Organism_taxid: 5062
Resolution:
2.00Å     R-factor:   0.160    
Authors: I.Zegers,P.Verhelst,C.W.Choe,J.Steyaert,U.Heinemann,L.Wyns,W.Saenger
Key ref:
I.Zegers et al. (1992). Role of histidine-40 in ribonuclease T1 catalysis: three-dimensionalstructures of the partially active His40Lys mutant. Biochemistry, 31, 11317-11325. PubMed id: 1445870 DOI: 10.1021/bi00161a009
Date:
15-Sep-92     Release date:   31-Jan-94    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00651  (RNT1_ASPOR) -  Guanyl-specific ribonuclease T1 from Aspergillus oryzae (strain ATCC 42149 / RIB 40)
Seq:
Struc: 		130 a.a.
104 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.6.1.24  - ribonuclease T1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

 

 
DOI no: 10.1021/bi00161a009 Biochemistry 31:11317-11325 (1992)
PubMed id: 1445870  
 
 
Role of histidine-40 in ribonuclease T1 catalysis: three-dimensionalstructures of the partially active His40Lys mutant.
I.Zegers, P.Verhelst, H.W.Choe, J.Steyaert, U.Heinemann, W.Saenger, L.Wyns.
 
  ABSTRACT  
 
Histidine-40 is known to participate in phosphodiester transesterification catalyzed by the enzyme ribonuclease T1. A mutant enzyme with a lysine replacing the histidine-40 (His40Lys RNase T1) retains considerable catalytic activity [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072]. We report on the crystal structures of His40Lys RNase T1 containing a phosphate anion and a guanosine 2'-phosphate inhibitor in the active site, respectively. Similar to previously described structures, the phosphate-containing crystals are of space group P2(1)2(1)2(1), with one molecule per asymmetric unit (a = 48.27 A, b = 46.50 A, c = 41.14 A). The complex with 2'-GMP crystallized in the lower symmetry space group P2(1), with two molecules per asymmetric unit (a = 49.20 A, b = 48.19 A, c = 40.16 A, beta = 90.26). The crystal structures have been solved at 1.8- and 2.0-A resolution yielding R values of 14.5% and 16.0%, respectively. Comparison of these His40Lys structures with the corresponding wild-type structures, containing 2'-GMP [Arni, R., Heinemann, U., Tokuoka, R., & Saenger, W. (1988) J. Biol. Chem. 263, 15358-15368] and vanadate [Kostrewa, D., Hui-Woog Choe, Heinemann, U., & Saenger, W. (1989) Biochemistry 28, 7692-7600] in the active site, respectively, leads to the following conclusions. First, the His40Lys mutation causes no significant changes in the overall structure of RNase T1; second, the Lys40 side chains in the mutant structures occupy roughly the same space as His40 in the corresponding wild-type RNase T1 structures.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21199564 A.S.Dielen, F.T.Sassaki, J.Walter, T.Michon, G.Ménard, G.Pagny, R.Krause-Sakate, I.d.e. .G.Maia, S.Badaoui, O.Le Gall, T.Candresse, and S.German-Retana (2011).
The 20S proteasome α5 subunit of Arabidopsis thaliana carries an RNase activity and interacts in planta with the Lettuce mosaic potyvirus HcPro protein.
  Mol Plant Pathol, 12, 137-150.  
11530931 T.Greiner-Stöffele, H.H.Förster, H.J.Hofmann, and U.Hahn (2001).
RNase-stable RNA: conformational parameters of the nucleic acid backbone for binding to RNase T1.
  Biol Chem, 382, 1007-1017.  
  9385633 A.C.Wallace, N.Borkakoti, and J.M.Thornton (1997).
TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.
  Protein Sci, 6, 2308-2323.  
9249002 J.Steyaert (1997).
A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions.
  Eur J Biochem, 247, 1.  
  8844843 J.Doumen, M.Gonciarz, I.Zegers, R.Loris, L.Wyns, and J.Steyaert (1996).
A catalytic function for the structurally conserved residue Phe 100 of ribonuclease T1.
  Protein Sci, 5, 1523-1530.
PDB code: 1bir
8805570 X.Yang, and K.Moffat (1996).
Insights into specificity of cleavage and mechanism of cell entry from the crystal structure of the highly specific Aspergillus ribotoxin, restrictocin.
  Structure, 4, 837-852.
PDB code: 1aqz
8125111 W.D.Schubert, G.Schluckebier, J.Backmann, J.Granzin, C.Kisker, H.W.Choe, U.Hahn, W.Pfeil, and W.Saenger (1994).
X-ray crystallographic and calorimetric studies of the effects of the mutation Trp59-->Tyr in ribonuclease T1.
  Eur J Biochem, 220, 527-534.
PDB codes: 1trp 1trq
8281918 A.Heydenreich, G.Koellner, H.W.Choe, F.Cordes, C.Kisker, H.Schindelin, R.Adamiak, U.Hahn, and W.Saenger (1993).
The complex between ribonuclease T1 and 3'GMP suggests geometry of enzymic reaction path. An X-ray study.
  Eur J Biochem, 218, 1005-1012.
PDB code: 1rgc
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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