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PDBsum entry 1dy5

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1dy5
Jmol
Contents
Protein chains
124 a.a. *
Ligands
SO4 ×3
ACT ×4
IPA ×8
Waters ×381
* Residue conservation analysis
PDB id:
1dy5
Name: Hydrolase
Title: Deamidated derivative of bovine pancreatic ribonuclease
Structure: Ribonuclease a. Chain: a, b. Mutation: yes. Other_details: asn 67 replaced by a beta-aspartyl residue
Source: Bos taurus. Bovine. Organism_taxid: 9913. Organ: pancreas
Resolution:
0.87Å     R-factor:   0.101     R-free:   0.119
Authors: L.Esposito,L.Vitagliano,F.Sica,A.Zagari,L.Mazzarella
Key ref:
L.Esposito et al. (2000). The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol, 297, 713-732. PubMed id: 10731423 DOI: 10.1006/jmbi.2000.3597
Date:
27-Jan-00     Release date:   28-Mar-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
124 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - 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   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1006/jmbi.2000.3597 J Mol Biol 297:713-732 (2000)
PubMed id: 10731423  
 
 
The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis.
L.Esposito, L.Vitagliano, F.Sica, G.Sorrentino, A.Zagari, L.Mazzarella.
 
  ABSTRACT  
 
Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Electron density for hydrogen atoms. (a) F[o] -F[c] map (magenta) around His12 calculated before the inclusion of hydrogen atoms in the refinement and contoured at a level of 1.7s. The difference map is superimposed to the 3F[o] -2F[c] map contoured at a level of 3.7s (cyan). (b) F[o] -F[c] map (at 3sigma level) showing H atoms involved in CA--H...O contacts in beta-sheet regions. The map has been calculated from the final model omitting all the hydrogen atoms.
Figure 4.
Figure 4. Isoaspartyl residue environment. (a) Carboxyl-carboxylate interaction between Glu A86 and isoAsp B67. Electron density map with coefficients (3F[o] -2F[c]) is contoured at 2.4sigma. (b) Highly defined electron density map in the region of the Cys A65-Cys A72 loop (contour level 2.8sigma).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 713-732) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20623666 S.Noguchi (2010).
Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B.
  Biopolymers, 93, 1003-1010.
PDB code: 3ahs
21123875 W.G.Touw, and G.Vriend (2010).
On the complexity of Engh and Huber refinement restraints: the angle τ as example.
  Acta Crystallogr D Biol Crystallogr, 66, 1341-1350.  
19137577 K.Okuyama, C.Hongo, G.Wu, K.Mizuno, K.Noguchi, S.Ebisuzaki, Y.Tanaka, N.Nishino, and H.P.Bächinger (2009).
High-resolution structures of collagen-like peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4)]: Implications for triple-helix hydration and Hyp(X) puckering.
  Biopolymers, 91, 361-372.
PDB codes: 2d3f 2d3h
18586714 I.Georgiev, D.Keedy, J.S.Richardson, D.C.Richardson, and B.R.Donald (2008).
Algorithm for backrub motions in protein design.
  Bioinformatics, 24, i196-i204.  
18566511 R.M.Coman, A.H.Robbins, M.M.Goodenow, B.M.Dunn, and R.McKenna (2008).
High-resolution structure of unbound human immunodeficiency virus 1 subtype C protease: implications of flap dynamics and drug resistance.
  Acta Crystallogr D Biol Crystallogr, 64, 754-763.
PDB code: 2r8n
18710925 T.A.Springer, J.Zhu, and T.Xiao (2008).
Structural basis for distinctive recognition of fibrinogen gammaC peptide by the platelet integrin alphaIIbbeta3.
  J Cell Biol, 182, 791-800.
PDB codes: 2vc2 2vdk 2vdl 2vdm 2vdn 2vdo 2vdp 2vdq 2vdr
17881830 B.Stec (2007).
Comment on Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? by Jaskolski, Gilski, Dauter & Wlodawer (2007).
  Acta Crystallogr D Biol Crystallogr, 63, 1113-1114.  
17292835 D.A.Kondrashov, A.W.Van Wynsberghe, R.M.Bannen, Q.Cui, and G.N.Phillips (2007).
Protein structural variation in computational models and crystallographic data.
  Structure, 15, 169-177.  
18084073 J.Wang, M.Dauter, R.Alkire, A.Joachimiak, and Z.Dauter (2007).
Triclinic lysozyme at 0.65 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 1254-1268.
PDB code: 2vb1
17452786 M.Jaskolski, M.Gilski, Z.Dauter, and A.Wlodawer (2007).
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
  Acta Crystallogr D Biol Crystallogr, 63, 611-620.  
17372355 M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 500-507.
PDB code: 2ayw
17080462 M.V.Shapovalov, and R.L.Dunbrack (2007).
Statistical and conformational analysis of the electron density of protein side chains.
  Proteins, 66, 279-303.  
16790925 N.Narayana (2006).
High-resolution structure of a plasmid-encoded dihydrofolate reductase: pentagonal network of water molecules in the D2-symmetric active site.
  Acta Crystallogr D Biol Crystallogr, 62, 695-706.
PDB code: 2gqv
15728177 A.Merlino, L.Mazzarella, A.Carannante, A.Di Fiore, A.Di Donato, E.Notomista, and F.Sica (2005).
The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants.
  J Biol Chem, 280, 17953-17960.
PDB codes: 1yv4 1yv6 1yv7
16301790 D.E.Holloway, G.B.Chavali, M.C.Hares, V.Subramanian, and K.R.Acharya (2005).
Structure of murine angiogenin: features of the substrate- and cell-binding regions and prospects for inhibitor-binding studies.
  Acta Crystallogr D Biol Crystallogr, 61, 1568-1578.
PDB codes: 2bwk 2bwl
15983423 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
  Acta Crystallogr D Biol Crystallogr, 61, 990.
PDB codes: 1yk4 1yk5
15048772 A.Merlino, L.Vitagliano, F.Sica, A.Zagari, and L.Mazzarella (2004).
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
  Biopolymers, 73, 689-695.
PDB codes: 1r5c 1r5d
15051877 B.Halle (2004).
Biomolecular cryocrystallography: structural changes during flash-cooling.
  Proc Natl Acad Sci U S A, 101, 4793-4798.  
15306377 B.Halle (2004).
Protein hydration dynamics in solution: a critical survey.
  Philos Trans R Soc Lond B Biol Sci, 359, 1207.  
15281129 K.Manikandan, and S.Ramakumar (2004).
The occurrence of C--H...O hydrogen bonds in alpha-helices and helix termini in globular proteins.
  Proteins, 56, 768-781.  
12756610 A.T.García-Sosa, R.L.Mancera, and P.M.Dean (2003).
WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.
  J Mol Model, 9, 172-182.  
12966091 G.Gotte, M.Libonati, and D.V.Laurents (2003).
Glycosylation and specific deamidation of ribonuclease B affect the formation of three-dimensional domain-swapped oligomers.
  J Biol Chem, 278, 46241-46251.  
12382288 A.Merlino, L.Vitagliano, M.A.Ceruso, A.Di Nola, and L.Mazzarella (2002).
Global and local motions in ribonuclease A: a molecular dynamics study.
  Biopolymers, 65, 274-283.  
11847284 C.D.Smith, M.Carson, A.M.Friedman, M.M.Skinner, L.Delucas, L.Chantalat, L.Weise, T.Shirasawa, and D.Chattopadhyay (2002).
Crystal structure of human L-isoaspartyl-O-methyl-transferase with S-adenosyl homocysteine at 1.6-A resolution and modeling of an isoaspartyl-containing peptide at the active site.
  Protein Sci, 11, 625-635.
PDB code: 1i1n
11943548 C.Mattos (2002).
Protein-water interactions in a dynamic world.
  Trends Biochem Sci, 27, 203-208.  
11876642 G.J.Swaminathan, D.E.Holloway, K.Veluraja, and K.R.Acharya (2002).
Atomic resolution (0.98 A) structure of eosinophil-derived neurotoxin.
  Biochemistry, 41, 3341-3352.
PDB code: 1gqv
11856829 R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, and L.Mazzarella (2002).
Atomic resolution structures of ribonuclease A at six pH values.
  Acta Crystallogr D Biol Crystallogr, 58, 441-450.
PDB codes: 1kf2 1kf3 1kf4 1kf5 1kf7 1kf8
11790836 R.Berisio, L.Vitagliano, L.Mazzarella, and A.Zagari (2002).
Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3).
  Protein Sci, 11, 262-270.
PDB code: 1k6f
12198301 R.Thaimattam, E.Tykarska, A.Bierzynski, G.M.Sheldrick, and M.Jaskolski (2002).
Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
  Acta Crystallogr D Biol Crystallogr, 58, 1448-1461.
PDB code: 1lu0
11320305 A.Addlagatta, S.Krzywda, H.Czapinska, J.Otlewski, and M.Jaskolski (2001).
Ultrahigh-resolution structure of a BPTI mutant.
  Acta Crystallogr D Biol Crystallogr, 57, 649-663.
PDB code: 1g6x
11288180 B.Das, and H.Meirovitch (2001).
Optimization of solvation models for predicting the structure of surface loops in proteins.
  Proteins, 43, 303-314.  
11173498 R.Berisio, A.Viguera, L.Serrano, and M.Wilmanns (2001).
Atomic resolution structure of a mutant of the spectrin SH3 domain.
  Acta Crystallogr D Biol Crystallogr, 57, 337-340.
PDB code: 1g2b
  11106179 L.Esposito, L.Vitagliano, A.Zagari, and L.Mazzarella (2000).
Pyramidalization of backbone carbonyl carbon atoms in proteins.
  Protein Sci, 9, 2038-2042.  
11009618 M.Ruoppolo, F.Vinci, T.A.Klink, R.T.Raines, and G.Marino (2000).
Contribution of individual disulfide bonds to the oxidative folding of ribonuclease A.
  Biochemistry, 39, 12033-12042.  
11070081 R.V.Pappu, R.Srinivasan, and G.D.Rose (2000).
The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.
  Proc Natl Acad Sci U S A, 97, 12565-12570.  
  11206080 S.Orrù, L.Vitagliano, L.Esposito, L.Mazzarella, G.Marino, and M.Ruoppolo (2000).
Effect of deamidation on folding of ribonuclease A.
  Protein Sci, 9, 2577-2582.  
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.