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Hydrolase PDB id
1snd
Jmol
Contents
Protein chains
129 a.a. *
Waters ×138
* Residue conservation analysis
PDB id:
1snd
Name: Hydrolase
Title: Staphylococcal nuclease dimer containing a deletion of resid 119 complexed with calcium chloride and the competitive inh deoxythymidine-3',5'-diphosphate
Structure: Staphylococcal nuclease dimer. Chain: a, b. Engineered: yes. Mutation: yes. Other_details: although the ligands were added for crystall they were not observed in the electron density maps and wer included in the final structure
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: foggi. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.84Å     R-factor:   0.176    
Authors: S.M.Green,A.G.Gittis,A.K.Meeker,E.E.Lattman
Key ref: S.M.Green et al. (1995). One-step evolution of a dimer from a monomeric protein. Nat Struct Biol, 2, 746-751. PubMed id: 7552745 DOI: 10.1038/nsb0995-746
Date:
23-Aug-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00644  (NUC_STAAU) -  Thermonuclease
Seq:
Struc: 		231 a.a.
129 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.31.1  - Micrococcal nuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     3 terms  

 

 
DOI no: 10.1038/nsb0995-746 Nat Struct Biol 2:746-751 (1995)
PubMed id: 7552745  
 
 
One-step evolution of a dimer from a monomeric protein.
S.M.Green, A.G.Gittis, A.K.Meeker, E.E.Lattman.
 
  ABSTRACT  
 
Deletion of six amino acids in a surface loop transforms staphylococcal nuclease from a monomeric protein into a very stable dimer (Kd < 1 x 10(-8)M). A 2 A X-ray crystal structure of the dimer (R = 0.176) shows that the carboxy-terminal alpha-helix has been stripped from its normal position in one monomer and is now incorporated into the equivalent position on the adjoining monomer. This swapping creates an association interface of 2900 A 2. A second, smaller interface of 460 A 2 is also formed. The spontaneous exchange or swapping of secondary structural elements provides a simple pathway for the formation of large, stable protein/protein interfaces and may play an important role in the evolution of oligomeric proteins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20976204 C.H.Chu, W.C.Lo, H.W.Wang, Y.C.Hsu, J.K.Hwang, P.C.Lyu, T.W.Pai, and C.Y.Tang (2010).
Detection and alignment of 3D domain swapping proteins using angle-distance image-based secondary structural matching techniques.
  PLoS One, 5, e13361.  
20064164 D.Guymer, J.Maillard, M.F.Agacan, C.A.Brearley, and F.Sargent (2010).
Intrinsic GTPase activity of a bacterial twin-arginine translocation proofreading chaperone induced by domain swapping.
  FEBS J, 277, 511-525.  
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
19299503 K.Sato, C.Li, I.Salard, A.J.Thompson, M.J.Banfield, and C.Dennison (2009).
Metal-binding loop length and not sequence dictates structure.
  Proc Natl Acad Sci U S A, 106, 5616-5621.
PDB codes: 3fs9 3fsa 3fsv 3fsw 3fsz 3ft0
19683009 Z.Qian, J.R.Horton, X.Cheng, and S.Lutz (2009).
Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.
  J Mol Biol, 393, 191-201.
PDB codes: 3icv 3icw
18395225 S.Posy, L.Shapiro, and B.Honig (2008).
Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface?
  J Mol Biol, 378, 954-968.  
17661445 E.Watson, W.M.Matousek, E.L.Irimies, and A.T.Alexandrescu (2007).
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins.
  Biochemistry, 46, 9484-9494.  
17897942 J.Wu, Y.Yang, J.Zhang, P.Ji, W.Du, P.Jiang, D.Xie, H.Huang, M.Wu, G.Zhang, J.Wu, and Y.Shi (2007).
Domain-swapped dimerization of the second PDZ domain of ZO2 may provide a structural basis for the polymerization of claudins.
  J Biol Chem, 282, 35988-35999.
PDB code: 2osg
17391511 V.Alva, M.Ammelburg, J.Söding, and A.N.Lupas (2007).
On the origin of the histone fold.
  BMC Struct Biol, 7, 17.  
16407060 F.Ding, K.C.Prutzman, S.L.Campbell, and N.V.Dokholyan (2006).
Topological determinants of protein domain swapping.
  Structure, 14, 5.  
16698543 M.J.Bennett, M.R.Sawaya, and D.Eisenberg (2006).
Deposition diseases and 3D domain swapping.
  Structure, 14, 811-824.  
15987889 K.Vamvaca, M.Butz, K.U.Walter, S.V.Taylor, and D.Hilvert (2005).
Simultaneous optimization of enzyme activity and quaternary structure by directed evolution.
  Protein Sci, 14, 2103-2114.  
15162492 A.T.Alexandrescu (2004).
Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints.
  Proteins, 56, 117-129.  
15180998 S.H.Liaw, Y.J.Chang, C.T.Lai, H.C.Chang, and G.G.Chang (2004).
Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily.
  J Biol Chem, 279, 35479-35485.
PDB code: 1wkq
15189881 S.Kundu, and R.L.Jernigan (2004).
Molecular mechanism of domain swapping in proteins: an analysis of slower motions.
  Biophys J, 86, 3846-3854.  
  12623012 F.Rousseau, J.W.Schymkowitz, and L.S.Itzhaki (2003).
The unfolding story of three-dimensional domain swapping.
  Structure, 11, 243-251.  
12598646 K.R.LeFevre, and M.H.Cordes (2003).
Retroevolution of lambda Cro toward a stable monomer.
  Proc Natl Acad Sci U S A, 100, 2345-2350.  
12084052 G.D'Alessio (2002).
The evolution of monomeric and oligomeric betagamma-type crystallins. Facts and hypotheses.
  Eur J Biochem, 269, 3122-3130.  
12356717 P.Verdino, K.Westritschnig, R.Valenta, and W.Keller (2002).
The cross-reactive calcium-binding pollen allergen, Phl p 7, reveals a novel dimer assembly.
  EMBO J, 21, 5007-5016.
PDB code: 1k9u
  12079775 S.L.Michel, and J.M.Berg (2002).
Building a metal binding domain, one half at a time.
  Chem Biol, 9, 667-668.  
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
11589702 B.Collinet, P.Garcia, P.Minard, and M.Desmadril (2001).
Role of loops in the folding and stability of yeast phosphoglycerate kinase.
  Eur J Biochem, 268, 5107-5118.  
11526208 B.Kuhlman, J.W.O'Neill, D.E.Kim, K.Y.Zhang, and D.Baker (2001).
Conversion of monomeric protein L to an obligate dimer by computational protein design.
  Proc Natl Acad Sci U S A, 98, 10687-10691.
PDB code: 1jml
11344301 F.Rousseau, J.W.Schymkowitz, H.R.Wilkinson, and L.S.Itzhaki (2001).
Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues.
  Proc Natl Acad Sci U S A, 98, 5596-5601.  
  11709166 J.W.O'Neill, D.E.Kim, K.Johnsen, D.Baker, and K.Y.Zhang (2001).
Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus.
  Structure, 9, 1017-1027.
PDB codes: 1k50 1k51 1k52 1k53
11171963 N.L.Ogihara, G.Ghirlanda, J.W.Bryson, M.Gingery, W.F.DeGrado, and D.Eisenberg (2001).
Design of three-dimensional domain-swapped dimers and fibrous oligomers.
  Proc Natl Acad Sci U S A, 98, 1404-1409.
PDB code: 1g6u
11592132 S.V.Taylor, P.Kast, and D.Hilvert (2001).
Investigating and Engineering Enzymes by Genetic Selection.
  Angew Chem Int Ed Engl, 40, 3310-3335.  
11025544 K.T.O'Neil, A.C.Bach, and W.F.DeGrado (2000).
Structural consequences of an amino acid deletion in the B1 domain of protein G.
  Proteins, 41, 323-333.  
10736157 N.Russo, A.Antignani, and G.D'Alessio (2000).
In vitro evolution of a dimeric variant of human pancreatic ribonuclease.
  Biochemistry, 39, 3585-3591.  
  10545323 T.Shirai, C.Mitsuyama, Y.Niwa, Y.Matsui, H.Hotta, T.Yamane, H.Kamiya, C.Ishii, T.Ogawa, and K.Muramoto (1999).
High-resolution structure of the conger eel galectin, congerin I, in lactose-liganded and ligand-free forms: emergence of a new structure class by accelerated evolution.
  Structure, 7, 1223-1233.
PDB codes: 1c1f 1c1l
  10210194 V.N.Uversky, A.S.Karnoup, R.Khurana, D.J.Segel, S.Doniach, and A.L.Fink (1999).
Association of partially-folded intermediates of staphylococcal nuclease induces structure and stability.
  Protein Sci, 8, 161-173.  
  9761479 A.J.Constans, M.R.Mayer, S.F.Sukits, and J.T.Lecomte (1998).
A test of the relationship between sequence and structure in proteins: excision of the heme binding site in apocytochrome b5.
  Protein Sci, 7, 1983-1993.  
9671502 A.P.Saint-Jean, K.R.Phillips, D.J.Creighton, and M.J.Stone (1998).
Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.
  Biochemistry, 37, 10345-10353.  
  10082372 G.MacBeath, P.Kast, and D.Hilvert (1998).
Probing enzyme quaternary structure by combinatorial mutagenesis and selection.
  Protein Sci, 7, 1757-1767.  
9666333 R.B.Russell, and C.P.Ponting (1998).
Protein fold irregularities that hinder sequence analysis.
  Curr Opin Struct Biol, 8, 364-371.  
9576907 V.N.Uversky, D.J.Segel, S.Doniach, and A.L.Fink (1998).
Association-induced folding of globular proteins.
  Proc Natl Acad Sci U S A, 95, 5480-5483.  
9204285 J.Heringa, and W.R.Taylor (1997).
Three-dimensional domain duplication, swapping and stealing.
  Curr Opin Struct Biol, 7, 416-421.  
8901871 M.A.Bianchet, G.Bains, P.Pelosi, J.Pevsner, S.H.Snyder, H.L.Monaco, and L.M.Amzel (1996).
The three-dimensional structure of bovine odorant binding protein and its mechanism of odor recognition.
  Nat Struct Biol, 3, 934-939.
PDB code: 1pbo
  8805536 N.Khazanovich, K.Bateman, M.Chernaia, M.Michalak, and M.James (1996).
Crystal structure of the yeast cell-cycle control protein, p13suc1, in a strand-exchanged dimer.
  Structure, 4, 299-309.
PDB code: 1puc
8901862 S.Brownlow, and L.Sawyer (1996).
Waiting to inhale.
  Nat Struct Biol, 3, 902-906.  
  8580836 M.J.Bennett, M.P.Schlunegger, and D.Eisenberg (1995).
3D domain swapping: a mechanism for oligomer assembly.
  Protein Sci, 4, 2455-2468.  
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.