PDBsum entry 2e0m

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protein metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chain
128 a.a. *
_CD ×8
_CL ×11
Waters ×390
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Mutant human ribonuclease 1 (t24l, q28l, r31l, r32l)
Structure: Ribonuclease. Chain: a, b. Synonym: ribonuclease 1, rnase 1, rnase a, rnase upi-1, rib rnase. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.70Å     R-factor:   0.195     R-free:   0.214
Authors: H.Yamada,T.Tamada,M.Kosaka,R.Kuroki
Key ref:
H.Yamada et al. (2007). 'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines. Protein Sci, 16, 1389-1397. PubMed id: 17586772 DOI: 10.1110/ps.072851407
10-Oct-06     Release date:   28-Aug-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic
156 a.a.
128 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  


DOI no: 10.1110/ps.072851407 Protein Sci 16:1389-1397 (2007)
PubMed id: 17586772  
'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines.
H.Yamada, T.Tamada, M.Kosaka, K.Miyata, S.Fujiki, M.Tano, M.Moriya, M.Yamanishi, E.Honjo, H.Tada, T.Ino, H.Yamaguchi, J.Futami, M.Seno, T.Nomoto, T.Hirata, M.Yoshimura, R.Kuroki.
A protein crystal lattice consists of surface contact regions, where the interactions of specific groups play a key role in stabilizing the regular arrangement of the protein molecules. In an attempt to control protein incorporation in a crystal lattice, a leucine zipper-like hydrophobic interface (comprising four leucine residues) was introduced into a helical region (helix 2) of the human pancreatic ribonuclease 1 (RNase 1) that was predicted to form a suitable crystallization interface. Although crystallization of wild-type RNase 1 has not yet been reported, the RNase 1 mutant having four leucines (4L-RNase 1) was successfully crystallized under several different conditions. The crystal structures were subsequently determined by X-ray crystallography by molecular replacement using the structure of bovine RNase A. The overall structure of 4L-RNase 1 is quite similar to that of the bovine RNase A, and the introduced leucine residues formed the designed crystal interface. To characterize the role of the introduced leucine residues in crystallization of RNase 1 further, the number of leucines was reduced to three or two (3L- and 2L-RNase 1, respectively). Both mutants crystallized and a similar hydrophobic interface as in 4L-RNase 1 was observed. A related approach to engineer crystal contacts at helix 3 of RNase 1 (N4L-RNase 1) was also evaluated. N4L-RNase 1 also successfully crystallized and formed the expected hydrophobic packing interface. These results suggest that appropriate introduction of a leucine zipper-like hydrophobic interface can promote intermolecular symmetry for more efficient protein crystallization in crystal lattice engineering efforts.
  Selected figure(s)  
Figure 3.
Figure 3. Packing regions in a2- or a3-helices are enlarged. (A) 4L-, (B)
  The above figure is reprinted by permission from the Protein Society: Protein Sci (2007, 16, 1389-1397) copyright 2007.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082721 G.J.Forse, N.Ram, D.R.Banatao, D.Cascio, M.R.Sawaya, H.E.Klock, S.A.Lesley, and T.O.Yeates (2011).
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.
  Protein Sci, 20, 168-178.
PDB code: 3o7o
20179335 M.Guo, R.Shapiro, P.Schimmel, and X.L.Yang (2010).
Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase.
  Acta Crystallogr D Biol Crystallogr, 66, 243-250.  
20506323 P.Sledz, H.Zheng, K.Murzyn, M.Chruszcz, M.D.Zimmerman, M.D.Chordia, A.Joachimiak, and W.Minor (2010).
New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.
  Protein Sci, 19, 1395-1404.  
20006621 R.K.Montange, E.Mondragón, D.van Tyne, A.D.Garst, P.Ceres, and R.T.Batey (2010).
Discrimination between closely related cellular metabolites by the SAM-I riboswitch.
  J Mol Biol, 396, 761-772.
PDB codes: 3gx2 3gx3 3gx5 3gx6 3gx7
  19177350 A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, and F.Sica (2009).
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
  Protein Sci, 18, 50-57.
PDB code: 3f8g
  19342785 T.Shimamura, Y.Nitanai, T.Uchiyama, and H.Matsuzawa (2009).
Improvement of crystal quality by surface mutations of beta-lactamase Toho-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 379-382.
PDB code: 2zq8
18421160 E.Honjo, T.Tamada, M.Adachi, R.Kuroki, A.Meher, and M.Blaber (2008).
Mutagenesis of the crystal contact of acidic fibroblast growth factor.
  J Synchrotron Radiat, 15, 285-287.  
18931409 H.Mizutani, K.Saraboji, S.M.Malathy Sony, M.N.Ponnuswamy, T.Kumarevel, B.S.Krishna Swamy, D.K.Simanshu, M.R.Murthy, and N.Kunishima (2008).
Systematic study on crystal-contact engineering of diphthine synthase: influence of mutations at crystal-packing regions on X-ray diffraction quality.
  Acta Crystallogr D Biol Crystallogr, 64, 1020-1033.  
18812515 M.S.Wilke, M.Heller, A.L.Creagh, C.A.Haynes, L.P.McIntosh, K.Poole, and N.C.Strynadka (2008).
The crystal structure of MexR from Pseudomonas aeruginosa in complex with its antirepressor ArmR.
  Proc Natl Acad Sci U S A, 105, 14832-14837.
PDB code: 3ech
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.