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PDBsum entry 2apq

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Hydrolase PDB id
2apq
Jmol
Contents
Protein chain
122 a.a. *
Ligands
PO4 ×2
Waters ×147
* Residue conservation analysis
PDB id:
2apq
Name: Hydrolase
Title: Crystal structure of an active site mutant of bovine pancreatic ribonuclease a (h119a-rnase a) with a 10- glutamine expansion in thE C-terminal hinge-loop.
Structure: Ribonuclease. Chain: a. Synonym: rnase 1, rnase a. Engineered: yes. Mutation: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Gene: rnase1, rns1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.181     R-free:   0.215
Authors: S.Sambashivan,Y.Liu,M.R.Sawaya,M.Gingery,D.Eisenberg
Key ref:
S.Sambashivan et al. (2005). Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure. Nature, 437, 266-269. PubMed id: 16148936 DOI: 10.1038/nature03916
Date:
16-Aug-05     Release date:   13-Sep-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
122 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: 10.1038/nature03916 Nature 437:266-269 (2005)
PubMed id: 16148936  
 
 
Amyloid-like fibrils of ribonuclease A with three-dimensional domain-swapped and native-like structure.
S.Sambashivan, Y.Liu, M.R.Sawaya, M.Gingery, D.Eisenberg.
 
  ABSTRACT  
 
Amyloid or amyloid-like fibrils are elongated, insoluble protein aggregates, formed in vivo in association with neurodegenerative diseases or in vitro from soluble native proteins, respectively. The underlying structure of the fibrillar or 'cross-beta' state has presented long-standing, fundamental puzzles of protein structure. These include whether fibril-forming proteins have two structurally distinct stable states, native and fibrillar, and whether all or only part of the native protein refolds as it converts to the fibrillar state. Here we show that a designed amyloid-like fibril of the well-characterized enzyme RNase A contains native-like molecules capable of enzymatic activity. In addition, these functional molecular units are formed from a core RNase A domain and a swapped complementary domain. These findings are consistent with the zipper-spine model in which a cross-beta spine is decorated with three-dimensional domain-swapped functional units, retaining native-like structure.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: RNase A monomer and C-terminal domain-swapped dimer and the 3D domain-swapped zipper-spine model. a, The RNase A monomer is stabilized by four disulphide bonds Cys 26 -Cys 84, Cys 40 -Cys 95, Cys 58 -Cys 110 and Cys 65 -Cys 72, hindering conformational changes. His 12 in the core of the protein and His 119 on the -strand that is swapped (shown by sticks) are active-site residues that we mutate to test for activity by complementation. b, The C-terminal domain-swapped dimer is formed by exchanging the C-terminal -strands between two monomers. The hinge loop (residues 112 -115) has been expanded by inserting the sequence -GQ[10]G-. c, Diagram of amyloid-like fibril formation in RNase A with Q[10] expansion, leading to a runaway domain swap. The Q[10]-H12A mutants are shown in blue and the Q[10]-H119A mutants in green. Domain swapping between two mutants complements active sites.
Figure 2.
Figure 2: Properties of the RNase A amyloid-like fibrils. The hinge-loop region of wild-type RNase A that connects the C-terminal -strand (triangle in the diagrams in column 1) to the protein core is expanded with the -GQ[10]G- motif to generate amyloid-forming RNase A mutants. Two inactive RNase A mutants are formed by replacing His 12 or His 119 with Ala. Wild-type RNase A does not form fibrils and has a fully functional active site (row 1, columns 2 and 4). The Q[10]-H12A, Q[10]-H119A and Q[10]-H12A + Q[10]-H119A constructs all form amyloid-like fibrils (column 2) and bind Congo red with the characteristic apple-green birefringence (column 3). The Q[10]-H12A + Q[10]-H119A fibrils (row 4, column 4) have significantly higher activity than fibrils of Q[10]-H12A (row 2, column 4) and Q[10]-H119A (row 3, column 4) alone. This is a result of complementation of active sites by domain swapping. The expected activity of each of the constructs is given in parentheses. Scale bar (column 2), 200 nm.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2005, 437, 266-269) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21131979 C.Liu, M.R.Sawaya, and D.Eisenberg (2011).
β₂-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.
  Nat Struct Mol Biol, 18, 49-55.
PDB codes: 3low 3loz
21220305 K.Domanska, S.Vanderhaegen, V.Srinivasan, E.Pardon, F.Dupeux, J.A.Marquez, S.Giorgetti, M.Stoppini, L.Wyns, V.Bellotti, and J.Steyaert (2011).
Atomic structure of a nanobody-trapped domain-swapped dimer of an amyloidogenic beta2-microglobulin variant.
  Proc Natl Acad Sci U S A, 108, 1314-1319.
PDB code: 2x89
20133726 L.Goldschmidt, P.K.Teng, R.Riek, and D.Eisenberg (2010).
Identifying the amylome, proteins capable of forming amyloid-like fibrils.
  Proc Natl Acad Sci U S A, 107, 3487-3492.  
20133689 M.Biancalana, K.Makabe, and S.Koide (2010).
Minimalist design of water-soluble cross-beta architecture.
  Proc Natl Acad Sci U S A, 107, 3469-3474.
PDB codes: 3cka 3eex
20091872 R.P.Nagarkar, R.A.Hule, D.J.Pochan, and J.P.Schneider (2010).
Domain swapping in materials design.
  Biopolymers, 94, 141-155.  
20615990 S.Hirota, Y.Hattori, S.Nagao, M.Taketa, H.Komori, H.Kamikubo, Z.Wang, I.Takahashi, S.Negi, Y.Sugiura, M.Kataoka, and Y.Higuchi (2010).
Cytochrome c polymerization by successive domain swapping at the C-terminal helix.
  Proc Natl Acad Sci U S A, 107, 12854-12859.
PDB codes: 3nbs 3nbt
20221255 S.R.McGuffee, and A.H.Elcock (2010).
Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.
  PLoS Comput Biol, 6, e1000694.  
19263489 C.Ercole, R.A.Colamarino, E.Pizzo, F.Fogolari, R.Spadaccini, and D.Picone (2009).
Comparison of the structural and functional properties of RNase A and BS-RNase: A stepwise mutagenesis approach.
  Biopolymers, 91, 1009-1017.  
19102631 D.Ramadan, P.C.Rancy, R.P.Nagarkar, J.P.Schneider, and C.Thorpe (2009).
Arsenic(III) species inhibit oxidative protein folding in vitro.
  Biochemistry, 48, 424-432.  
19027944 F.Guglielmi, D.M.Monti, A.Arciello, S.Torrassa, F.Cozzolino, P.Pucci, A.Relini, and R.Piccoli (2009).
Enzymatically active fibrils generated by the self-assembly of the ApoA-I fibrillogenic domain functionalized with a catalytic moiety.
  Biomaterials, 30, 829-835.  
19436956 I.J.Day, K.Maeda, H.J.Paisley, K.H.Mok, and P.J.Hore (2009).
Refolding of ribonuclease A monitored by real-time photo-CIDNP NMR spectroscopy.
  J Biomol NMR, 44, 77-86.  
19289061 J.Juárez, P.Taboada, and V.Mosquera (2009).
Existence of different structural intermediates on the fibrillation pathway of human serum albumin.
  Biophys J, 96, 2353-2370.  
19768682 J.Luo, A.Teplyakov, G.Obmolova, T.Malia, S.J.Wu, E.Beil, A.Baker, B.Swencki-Underwood, Y.Zhao, J.Sprenkle, K.Dixon, R.Sweet, and G.L.Gilliland (2009).
Structure of the EMMPRIN N-terminal domain 1: dimerization via beta-strand swapping.
  Proteins, 77, 1009-1014.
PDB codes: 3i84 3i85
19864624 M.I.Ivanova, S.A.Sievers, M.R.Sawaya, J.S.Wall, and D.Eisenberg (2009).
Molecular basis for insulin fibril assembly.
  Proc Natl Acad Sci U S A, 106, 18990-18995.
PDB code: 3hyd
19500970 M.J.Sippl (2009).
Fold space unlimited.
  Curr Opin Struct Biol, 19, 312-320.  
19602569 P.K.Teng, and D.Eisenberg (2009).
Short protein segments can drive a non-fibrillizing protein into the amyloid state.
  Protein Eng Des Sel, 22, 531-536.  
18849564 P.Mishra, and V.Bhakuni (2009).
Self-assembly of Bacteriophage-associated Hyaluronate Lyase (HYLP2) into an Enzymatically Active Fibrillar Film.
  J Biol Chem, 284, 5240-5249.  
19134476 S.Krishnan, and A.A.Raibekas (2009).
Multistep aggregation pathway of human interleukin-1 receptor antagonist: kinetic, structural, and morphological characterization.
  Biophys J, 96, 199-208.  
19011634 A.Y.Yam, Y.Xia, H.T.Lin, A.Burlingame, M.Gerstein, and J.Frydman (2008).
Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies.
  Nat Struct Mol Biol, 15, 1255-1262.  
17803210 G.Colombo, M.Meli, and A.De Simone (2008).
Computational studies of the structure, dynamics and native content of amyloid-like fibrils of ribonuclease A.
  Proteins, 70, 863-872.  
17763469 G.Cozza, S.Moro, and G.Gotte (2008).
Elucidation of the ribonuclease A aggregation process mediated by 3D domain swapping: a computational approach reveals possible new multimeric structures.
  Biopolymers, 89, 26-39.  
18083824 H.N.Otoo, K.G.Lee, W.Qiu, and P.N.Lipke (2008).
Candida albicans Als adhesins have conserved amyloid-forming sequences.
  Eukaryot Cell, 7, 776-782.  
18234827 L.Esposito, A.Paladino, C.Pedone, and L.Vitagliano (2008).
Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations.
  Biophys J, 94, 4031-4040.  
18684013 L.Wang, S.K.Maji, M.R.Sawaya, D.Eisenberg, and R.Riek (2008).
Bacterial inclusion bodies contain amyloid-like structure.
  PLoS Biol, 6, e195.  
18263661 M.Meli, G.Morra, and G.Colombo (2008).
Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations.
  Biophys J, 94, 4414-4426.  
18424511 M.Sackewitz, S.von Einem, G.Hause, M.Wunderlich, F.X.Schmid, and E.Schwarz (2008).
A folded and functional protein domain in an amyloid-like fibril.
  Protein Sci, 17, 1044-1054.  
17931593 R.V.Pappu, X.Wang, A.Vitalis, and S.L.Crick (2008).
A polymer physics perspective on driving forces and mechanisms for protein aggregation.
  Arch Biochem Biophys, 469, 132-141.  
17588526 T.R.Jahn, and S.E.Radford (2008).
Folding versus aggregation: polypeptide conformations on competing pathways.
  Arch Biochem Biophys, 469, 100-117.  
18537545 U.Baxa (2008).
Structural basis of infectious and non-infectious amyloids.
  Curr Alzheimer Res, 5, 308-318.  
18552127 Z.Guo, and D.Eisenberg (2008).
The structure of a fibril-forming sequence, NNQQNY, in the context of a globular fold.
  Protein Sci, 17, 1617-1623.
PDB code: 3cae
17376079 A.V.Zavialov, and S.D.Knight (2007).
A novel self-capping mechanism controls aggregation of periplasmic chaperone Caf1M.
  Mol Microbiol, 64, 153-164.
PDB code: 2os7
17242379 C.Iannuzzi, S.Vilasi, M.Portaccio, G.Irace, and I.Sirangelo (2007).
Heme binding inhibits the fibrillization of amyloidogenic apomyoglobin and determines lack of aggregate cytotoxicity.
  Protein Sci, 16, 507-516.  
17962398 J.Carey, S.Lindman, M.Bauer, and S.Linse (2007).
Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency.
  Protein Sci, 16, 2317-2333.  
17266726 K.E.Max, M.Zeeb, R.Bienert, J.Balbach, and U.Heinemann (2007).
Common mode of DNA binding to cold shock domains. Crystal structure of hexathymidine bound to the domain-swapped form of a major cold shock protein from Bacillus caldolyticus.
  FEBS J, 274, 1265-1279.
PDB code: 2hax
17468747 M.R.Sawaya, S.Sambashivan, R.Nelson, M.I.Ivanova, S.A.Sievers, M.I.Apostol, M.J.Thompson, M.Balbirnie, J.J.Wiltzius, H.T.McFarlane, A...Madsen, C.Riekel, and D.Eisenberg (2007).
Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
  Nature, 447, 453-457.
PDB codes: 2okz 2ol9 2olx 2omm 2omp 2omq 2on9 2ona 2onv 2onw 2onx
  19164912 M.T.Pastor, A.Esteras-Chopo, and L.Serrano (2007).
Hacking the code of amyloid formation: the amyloid stretch hypothesis.
  Prion, 1, 9.  
17470433 M.Wahlbom, X.Wang, V.Lindström, E.Carlemalm, M.Jaskolski, and A.Grubb (2007).
Fibrillogenic oligomers of human cystatin C are formed by propagated domain swapping.
  J Biol Chem, 282, 18318-18326.  
17450152 P.Li, K.E.Huey-Tubman, T.Gao, X.Li, A.P.West, M.J.Bennett, and P.J.Bjorkman (2007).
The structure of a polyQ-anti-polyQ complex reveals binding according to a linear lattice model.
  Nat Struct Mol Biol, 14, 381-387.
PDB code: 2gsg
17959784 R.Giraldo (2007).
Defined DNA sequences promote the assembly of a bacterial protein into distinct amyloid nanostructures.
  Proc Natl Acad Sci U S A, 104, 17388-17393.  
18096801 T.P.Knowles, A.W.Fitzpatrick, S.Meehan, H.R.Mott, M.Vendruscolo, C.M.Dobson, and M.E.Welland (2007).
Role of intermolecular forces in defining material properties of protein nanofibrils.
  Science, 318, 1900-1903.  
17391511 V.Alva, M.Ammelburg, J.Söding, and A.N.Lupas (2007).
On the origin of the histone fold.
  BMC Struct Biol, 7, 17.  
17704182 W.F.Weiss, T.K.Hodgdon, E.W.Kaler, A.M.Lenhoff, and C.J.Roberts (2007).
Nonnative protein polymers: structure, morphology, and relation to nucleation and growth.
  Biophys J, 93, 4392-4403.  
16491088 C.M.Eakin, A.J.Berman, and A.D.Miranker (2006).
A native to amyloidogenic transition regulated by a backbone trigger.
  Nat Struct Mol Biol, 13, 202-208.
PDB code: 2f8o
16765889 C.X.Weichenberger, and M.J.Sippl (2006).
Self-consistent assignment of asparagine and glutamine amide rotamers in protein crystal structures.
  Structure, 14, 967-972.  
16524841 D.Eisenberg, E.Marcotte, A.D.McLachlan, and M.Pellegrini (2006).
Bioinformatic challenges for the next decade(s).
  Philos Trans R Soc Lond B Biol Sci, 361, 525-527.  
16981672 D.Eisenberg, R.Nelson, M.R.Sawaya, M.Balbirnie, S.Sambashivan, M.I.Ivanova, A...Madsen, and C.Riekel (2006).
The structural biology of protein aggregation diseases: Fundamental questions and some answers.
  Acc Chem Res, 39, 568-575.  
16891363 I.K.Lednev, V.V.Ermolenkov, S.Higashiya, L.A.Popova, N.I.Topilina, and J.T.Welch (2006).
Reversible thermal denaturation of a 60-kDa genetically engineered beta-sheet polypeptide.
  Biophys J, 91, 3805-3818.  
16415350 J.P.López-Alonso, M.Bruix, J.Font, M.Ribó, M.Vilanova, M.Rico, G.Gotte, M.Libonati, C.González, and D.V.Laurents (2006).
Formation, structure, and dissociation of the ribonuclease S three-dimensional domain-swapped dimer.
  J Biol Chem, 281, 9400-9406.  
17093048 K.Makabe, D.McElheny, V.Tereshko, A.Hilyard, G.Gawlak, S.Yan, A.Koide, and S.Koide (2006).
Atomic structures of peptide self-assembly mimics.
  Proc Natl Acad Sci U S A, 103, 17753-17758.
PDB codes: 2af5 2fkg 2fkj 2hkd
16864786 L.Esposito, C.Pedone, and L.Vitagliano (2006).
Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation.
  Proc Natl Acad Sci U S A, 103, 11533-11538.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
16963458 M.R.Ho, Y.C.Lou, W.C.Lin, P.C.Lyu, W.N.Huang, and C.Chen (2006).
Human pancreatitis-associated protein forms fibrillar aggregates with a native-like conformation.
  J Biol Chem, 281, 33566-33576.
PDB code: 2go0
16519682 M.Rodríguez, A.Benito, M.Ribó, and M.Vilanova (2006).
Characterization of the dimerization process of a domain-swapped dimeric variant of human pancreatic ribonuclease.
  FEBS J, 273, 1166-1176.  
16675442 R.Bader, M.A.Seeliger, S.E.Kelly, L.L.Ilag, F.Meersman, A.Limones, B.F.Luisi, C.M.Dobson, and L.S.Itzhaki (2006).
Folding and fibril formation of the cell cycle protein Cks1.
  J Biol Chem, 281, 18816-18824.  
16563741 R.Nelson, and D.Eisenberg (2006).
Recent atomic models of amyloid fibril structure.
  Curr Opin Struct Biol, 16, 260-265.  
16488975 S.D.Khare, and N.V.Dokholyan (2006).
Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants.
  Proc Natl Acad Sci U S A, 103, 3147-3152.  
16636995 S.L.Myers, N.H.Thomson, S.E.Radford, and A.E.Ashcroft (2006).
Investigating the structural properties of amyloid-like fibrils formed in vitro from beta2-microglobulin using limited proteolysis and electrospray ionisation mass spectrometry.
  Rapid Commun Mass Spectrom, 20, 1628-1636.  
16491092 T.R.Jahn, M.J.Parker, S.W.Homans, and S.E.Radford (2006).
Amyloid formation under physiological conditions proceeds via a native-like folding intermediate.
  Nat Struct Mol Biol, 13, 195-201.  
16782819 X.Q.Mu, and E.Bullitt (2006).
Structure and assembly of P-pili: a protruding hinge region used for assembly of a bacterial adhesion filament.
  Proc Natl Acad Sci U S A, 103, 9861-9866.  
16698921 Z.Guo, and D.Eisenberg (2006).
Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I.
  Proc Natl Acad Sci U S A, 103, 8042-8047.  
16263932 A.Esteras-Chopo, L.Serrano, and M.López de la Paz (2005).
The amyloid stretch hypothesis: recruiting proteins toward the dark side.
  Proc Natl Acad Sci U S A, 102, 16672-16677.  
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 codes are shown on the right.