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PDBsum entry 104l

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protein Protein-protein interface(s) links
Hydrolase(o-glycosyl) PDB id
104l
Jmol
Contents
Protein chains
164 a.a. *
Waters ×32
* Residue conservation analysis
PDB id:
104l
Name: Hydrolase(o-glycosyl)
Title: How amino-acid insertions are allowed in an alpha-helix of t4 lysozyme
Structure: T4 lysozyme. Chain: a, b. Engineered: yes
Source: Enterobacteria phage t4. Organism_taxid: 10665.
Resolution:
2.80Å     R-factor:   0.175    
Authors: D.W.Heinz,B.W.Matthews
Key ref: D.W.Heinz et al. (1993). How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme. Nature, 361, 561-564. PubMed id: 8429913
Date:
29-Sep-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00720  (LYS_BPT4) -  Endolysin
Seq:
Struc:
164 a.a.
164 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.2.1.17  - Lysozyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of the prokaryotes cell walls.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cell wall macromolecule catabolic process   2 terms 
  Biochemical function     lysozyme activity     1 term  

 

 
Nature 361:561-564 (1993)
PubMed id: 8429913  
 
 
How amino-acid insertions are allowed in an alpha-helix of T4 lysozyme.
D.W.Heinz, W.A.Baase, F.W.Dahlquist, B.W.Matthews.
 
  ABSTRACT  
 
Studies of extant protein sequences indicate that amino-acid insertions and deletions are preferentially located in loop regions, which has traditionally been explained as the result of selection removing deleterious mutations within secondary structural elements from the population. But there is no a priori reason to discount the possibility that insertions within secondary structure could either be tolerated until compensatory mutations arise, or have effects that are propagated away from secondary structure into loops. Earlier studies have indicated that insertions are generally tolerated, although much less well within secondary structure elements than in loop regions. Here we show that amino-acid insertions in an alpha-helix of T4 lysozyme can be accepted in two different ways. In some cases the inserted amino acids are accommodated within the helix, leading to the translocation of wild-type residues from the helix to the preceding loop. In other cases the insertion causes a 'looping-out' in the first or last turn of the helix. The individual structural responses seem to be dominated by the maintenance of the interface between the helix and the rest of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20684774 R.Kim, and J.T.Guo (2010).
Systematic analysis of short internal indels and their impact on protein folding.
  BMC Struct Biol, 10, 24.  
20095051 W.A.Baase, L.Liu, D.E.Tronrud, and B.W.Matthews (2010).
Lessons from the lysozyme of phage T4.
  Protein Sci, 19, 631-641.  
19731372 D.A.Keedy, C.J.Williams, J.J.Headd, W.B.Arendall, V.B.Chen, G.J.Kapral, R.A.Gillespie, J.N.Block, A.Zemla, D.C.Richardson, and J.S.Richardson (2009).
The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.
  Proteins, 77, 29-49.  
19165724 V.A.Risso, M.E.Primo, and M.R.Ermácora (2009).
Re-engineering a beta-lactamase using prototype peptides from a library of local structural motifs.
  Protein Sci, 18, 440-449.  
19175938 Z.Wang, J.Martin, S.Abubucker, Y.Yin, R.B.Gasser, and M.Mitreva (2009).
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance.
  BMC Evol Biol, 9, 23.  
16597830 M.Sagermann, W.A.Baase, and B.W.Matthews (2006).
Sequential reorganization of beta-sheet topology by insertion of a single strand.
  Protein Sci, 15, 1085-1092.
PDB codes: 2b7w 2b7x 3jr6
15340919 C.L.Wilson, P.E.Boardman, A.J.Doig, and S.J.Hubbard (2004).
Improved prediction for N-termini of alpha-helices using empirical information.
  Proteins, 57, 322-330.  
14997564 E.Poussu, M.Vihinen, L.Paulin, and H.Savilahti (2004).
Probing the alpha-complementing domain of E. coli beta-galactosidase with use of an insertional pentapeptide mutagenesis strategy based on Mu in vitro DNA transposition.
  Proteins, 54, 681-692.  
15093829 G.Zhang (2004).
Tumor necrosis factor family ligand-receptor binding.
  Curr Opin Struct Biol, 14, 154-160.  
12626684 C.D.Pivetti, M.R.Yen, S.Miller, W.Busch, Y.H.Tseng, I.R.Booth, and M.H.Saier (2003).
Two families of mechanosensitive channel proteins.
  Microbiol Mol Biol Rev, 67, 66.  
12869697 M.Sagermann, L.Gay, and B.W.Matthews (2003).
Long-distance conformational changes in a protein engineered by modulated sequence duplication.
  Proc Natl Acad Sci U S A, 100, 9191-9195.
PDB code: 1oyu
14656435 S.G.Hymowitz, D.M.Compaan, M.Yan, H.J.Wallweber, V.M.Dixit, M.A.Starovasnik, and A.M.de Vos (2003).
The crystal structures of EDA-A1 and EDA-A2: splice variants with distinct receptor specificity.
  Structure, 11, 1513-1520.
PDB codes: 1rj7 1rj8
12360529 J.R.Beasley, D.F.Doyle, L.Chen, D.S.Cohen, B.R.Fine, and G.J.Pielak (2002).
Searching for quantitative entropy-enthalpy compensation among protein variants.
  Proteins, 49, 398-402.  
10681499 B.Schoepp, E.Chabaud, C.Breyton, A.Verméglio, and J.L.Popot (2000).
On the spatial organization of hemes and chlorophyll in cytochrome b(6)f. A linear and circular dichroism study.
  J Biol Chem, 275, 5275-5283.  
10861938 D.M.Nguyen, A.G.Gittis, and E.E.Lattman (2000).
The duplication of an eight-residue helical stretch in Staphylococcal nuclease is not helical: a model for evolutionary change.
  Proteins, 40, 465-472.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10339544 M.Sagermann, W.A.Baase, and B.W.Matthews (1999).
Structural characterization of an engineered tandem repeat contrasts the importance of context and sequence in protein folding.
  Proc Natl Acad Sci U S A, 96, 6078-6083.
PDB codes: 261l 262l
9529148 D.H.Fremont, D.Monnaie, C.A.Nelson, W.A.Hendrickson, and E.R.Unanue (1998).
Crystal structure of I-Ak in complex with a dominant epitope of lysozyme.
  Immunity, 8, 305-317.
PDB code: 1iak
9819220 R.Kuras, M.Guergova-Kuras, and A.R.Crofts (1998).
Steps toward constructing a cytochrome b6 f complex in the purple bacterium Rhodobacter sphaeroides: an example of the structural plasticity of a membrane cytochrome.
  Biochemistry, 37, 16280-16288.  
9016723 K.S.Thorn, H.E.Christensen, R.Shigeta, D.Huddler, L.Shalaby, U.Lindberg, N.H.Chua, and C.E.Schutt (1997).
The crystal structure of a major allergen from plants.
  Structure, 5, 19-32.
PDB codes: 1a0k 1plm 3nul
  8976549 I.R.Vetter, W.A.Baase, D.W.Heinz, J.P.Xiong, S.Snow, and B.W.Matthews (1996).
Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme.
  Protein Sci, 5, 2399-2415.
PDB codes: 209l 210l 211l 212l 213l 214l 215l 218l 219l
8889173 J.H.Carra, E.C.Murphy, and P.L.Privalov (1996).
Thermodynamic effects of mutations on the denaturation of T4 lysozyme.
  Biophys J, 71, 1994-2001.  
8547253 R.A.Albright, M.C.Mossing, and B.W.Matthews (1996).
High-resolution structure of an engineered Cro monomer shows changes in conformation relative to the native dimer.
  Biochemistry, 35, 735-742.
PDB code: 1orc
  7670375 A.J.Doig, and R.L.Baldwin (1995).
N- and C-capping preferences for all 20 amino acids in alpha-helical peptides.
  Protein Sci, 4, 1325-1336.  
  7815497 P.Poumbourios, W.el Ahmar, D.A.McPhee, and B.E.Kemp (1995).
Determinants of human immunodeficiency virus type 1 envelope glycoprotein oligomeric structure.
  J Virol, 69, 1209-1218.  
7607223 P.T.Harrison, J.E.Scott, M.J.Hutchinson, and R.Thompson (1995).
Site-directed mutagenesis of varicella-zoster virus thymidylate synthase. Analysis of two highly conserved regions of the enzyme.
  Eur J Biochem, 230, 511-516.  
7697723 R.B.Sutton, B.A.Davletov, A.M.Berghuis, T.C.Südhof, and S.R.Sprang (1995).
Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold.
  Cell, 80, 929-938.
PDB code: 1rsy
8078936 A.A.Fedorov, K.A.Magnus, M.H.Graupe, E.E.Lattman, T.D.Pollard, and S.C.Almo (1994).
X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates.
  Proc Natl Acad Sci U S A, 91, 8636-8640.
PDB codes: 1acf 2acg
  7833817 A.Sali, and J.P.Overington (1994).
Derivation of rules for comparative protein modeling from a database of protein structure alignments.
  Protein Sci, 3, 1582-1596.  
7765172 E.P.Baldwin, and B.W.Matthews (1994).
Core-packing constraints, hydrophobicity and protein design.
  Curr Opin Biotechnol, 5, 396-402.  
  7833813 P.Luginbühl, M.Ottiger, S.Mronga, and K.Wüthrich (1994).
Structure comparison of the pheromones Er-1, Er-10, and Er-2 from Euplotes raikovi.
  Protein Sci, 3, 1537-1546.  
7971148 T.E.Hebert, R.Monette, J.C.Stone, P.Drapeau, and R.J.Dunn (1994).
Insertion mutations of the RIIA Na+ channel reveal novel features of voltage gating and protein kinase A modulation.
  Pflugers Arch, 427, 500-509.  
8290361 M.P.Laget, I.Callebaut, Y.de Launoit, D.Stehelin, and J.P.Mornon (1993).
Predicted common structural features of DNA-binding domains from Ets, Myb and HMG transcription factors.
  Nucleic Acids Res, 21, 5987-5996.  
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.