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PDBsum entry 1enh

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protein links
DNA-binding protein PDB id
1enh
Jmol
Contents
Protein chain
54 a.a. *
Waters ×33
* Residue conservation analysis
PDB id:
1enh
Name: DNA-binding protein
Title: Structural studies of the engrailed homeodomain
Structure: Engrailed homeodomain. Chain: a. Engineered: yes
Source: Drosophila melanogaster. Fruit fly. Organism_taxid: 7227
Resolution:
2.10Å     R-factor:   0.197    
Authors: N.D.Clarke,C.R.Kissinger,J.Desjarlais,G.L.Gilliland,C.O.Pabo
Key ref: N.D.Clarke et al. (1994). Structural studies of the engrailed homeodomain. Protein Sci, 3, 1779-1787. PubMed id: 7849596 DOI: 10.1002/pro.5560031018
Date:
20-May-94     Release date:   31-Aug-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02836  (HMEN_DROME) -  Segmentation polarity homeobox protein engrailed
Seq:
Struc:
 
Seq:
Struc:
552 a.a.
54 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     transcription regulatory region sequence-specific DNA binding     4 terms  

 

 
DOI no: 10.1002/pro.5560031018 Protein Sci 3:1779-1787 (1994)
PubMed id: 7849596  
 
 
Structural studies of the engrailed homeodomain.
N.D.Clarke, C.R.Kissinger, J.Desjarlais, G.L.Gilliland, C.O.Pabo.
 
  ABSTRACT  
 
The structure of the Drosophila engrailed homeodomain has been solved by molecular replacement and refined to an R-factor of 19.7% at a resolution of 2.1 A. This structure offers a high-resolution view of an important family of DNA-binding proteins and allows comparison to the structure of the same protein bound to DNA. The most significant difference between the current structure and that of the 2.8-A engrailed-DNA complex is the close packing of an extended strand against the rest of the protein in the unbound protein. Structural features of the protein not previously noted include a "herringbone" packing of 4 aromatic residues in the core of the protein and an extensive network of salt bridges that covers much of the helix 1-helix 2 surface. Other features that may play a role in stabilizing the native state include the interaction of buried carbonyl oxygen atoms with the edge of Phe 49 and a bias toward statistically preferred side-chain dihedral angles. There is substantial disorder at both ends of the 61 amino acid protein. A 51-amino acid variant of engrailed (residues 6-56) was synthesized and shown by CD and thermal denaturation studies to be structurally and thermodynamically similar to the full-length domain.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20509910 L.E.Bird, J.Ren, J.E.Nettleship, G.E.Folkers, R.J.Owens, and D.K.Stammers (2010).
Novel structural features in two ZHX homeodomains derived from a systematic study of single and multiple domains.
  BMC Struct Biol, 10, 13.
PDB codes: 3nar 3nau
  20017135 U.Koz┼éowska, G.G.Maisuradze, A.Liwo, and H.A.Scheraga (2010).
Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field.
  J Comput Chem, 31, 1154-1167.  
19413955 A.Verma, and W.Wenzel (2009).
A free-energy approach for all-atom protein simulation.
  Biophys J, 96, 3483-3494.  
18506808 A.Vitalis, and R.V.Pappu (2009).
ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions.
  J Comput Chem, 30, 673-699.  
19445951 B.G.Wensley, M.Gärtner, W.X.Choo, S.Batey, and J.Clarke (2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
  J Mol Biol, 390, 1074-1085.  
19513117 G.R.Bowman, and V.S.Pande (2009).
The roles of entropy and kinetics in structure prediction.
  PLoS One, 4, e5840.  
19242966 Y.He, Y.Xiao, A.Liwo, and H.A.Scheraga (2009).
Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.
  J Comput Chem, 30, 2127-2135.  
17847091 A.F.Pereira de Araújo, A.L.Gomes, A.A.Bursztyn, and E.I.Shakhnovich (2008).
Native atomic burials, supplemented by physically motivated hydrogen bond constraints, contain sufficient information to determine the tertiary structure of small globular proteins.
  Proteins, 70, 971-983.  
18024496 D.W.Li, H.Yang, L.Han, and S.Huo (2008).
Predicting the folding pathway of engrailed homeodomain with a probabilistic roadmap enhanced reaction-path algorithm.
  Biophys J, 94, 1622-1629.  
18708527 O.Alvizo, and S.L.Mayo (2008).
Evaluating and optimizing computational protein design force fields using fixed composition-based negative design.
  Proc Natl Acad Sci U S A, 105, 12242-12247.  
18274703 T.L.Religa (2008).
Comparison of multiple crystal structures with NMR data for engrailed homeodomain.
  J Biomol NMR, 40, 189-202.
PDB code: 2jwt
17978165 D.A.Beck, and V.Daggett (2007).
A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.
  Biophys J, 93, 3382-3391.  
18154373 E.F.Koslover, and D.J.Wales (2007).
Geometry optimization for peptides and proteins: Comparison of Cartesian and internal coordinates.
  J Chem Phys, 127, 234105.  
17411115 M.J.Schnieders, N.A.Baker, P.Ren, and J.W.Ponder (2007).
Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum.
  J Chem Phys, 126, 124114.  
17517666 T.L.Religa, C.M.Johnson, D.M.Vu, S.H.Brewer, R.B.Dyer, and A.R.Fersht (2007).
The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain.
  Proc Natl Acad Sci U S A, 104, 9272-9277.
PDB code: 2p81
17236141 X.Zhao, M.Sun, J.Zhao, J.A.Leyva, H.Zhu, W.Yang, X.Zeng, Y.Ao, Q.Liu, G.Liu, W.H.Lo, E.W.Jabs, L.M.Amzel, X.Shan, and X.Zhang (2007).
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome.
  Am J Hum Genet, 80, 361-371.  
17095606 I.A.Hubner, E.J.Deeds, and E.I.Shakhnovich (2006).
Understanding ensemble protein folding at atomic detail.
  Proc Natl Acad Sci U S A, 103, 17747-17752.  
16943445 S.Lim, and S.J.Franklin (2006).
Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution.
  Protein Sci, 15, 2159-2165.  
15741348 G.K.Hom, J.K.Lassila, L.M.Thomas, and S.L.Mayo (2005).
Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant.
  Protein Sci, 14, 1115-1119.
PDB code: 1y66
16392943 J.M.Carr, and D.J.Wales (2005).
Global optimization and folding pathways of selected alpha-helical proteins.
  J Chem Phys, 123, 234901.  
15837204 T.Herges, and W.Wenzel (2005).
Free-energy landscape of the villin headpiece in an all-atom force field.
  Structure, 13, 661-668.  
16222301 T.L.Religa, J.S.Markson, U.Mayor, S.M.Freund, and A.R.Fersht (2005).
Solution structure of a protein denatured state and folding intermediate.
  Nature, 437, 1053-1056.
PDB code: 1ztr
15247345 M.D.Simon, K.Sato, G.A.Weiss, and K.M.Shokat (2004).
A phage display selection of engrailed homeodomain mutants and the importance of residue Q50.
  Nucleic Acids Res, 32, 3623-3631.  
15362137 P.S.Shah, G.K.Hom, and S.L.Mayo (2004).
Preprocessing of rotamers for protein design calculations.
  J Comput Chem, 25, 1797-1800.  
15507688 T.Herges, and W.Wenzel (2004).
An all-atom force field for tertiary structure prediction of helical proteins.
  Biophys J, 87, 3100-3109.  
12538894 A.Ke, and C.Wolberger (2003).
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.
  Protein Sci, 12, 306-312.
PDB codes: 1mh3 1mh4
12944263 G.Favrin, A.Irbäck, B.Samuelsson, and S.Wallin (2003).
Two-state folding over a weak free-energy barrier.
  Biophys J, 85, 1457-1465.  
12517448 V.Daggett, and A.R.Fersht (2003).
Is there a unifying mechanism for protein folding?
  Trends Biochem Sci, 28, 18-25.  
  10892804 K.Raha, A.M.Wollacott, M.J.Italia, and J.R.Desjarlais (2000).
Prediction of amino acid sequence from structure.
  Protein Sci, 9, 1106-1119.  
11003645 M.Kipp, F.Göhring, T.Ostendorp, C.M.van Drunen, R.van Driel, M.Przybylski, and F.O.Fackelmayer (2000).
SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA.
  Mol Cell Biol, 20, 7480-7489.  
11087839 U.Mayor, C.M.Johnson, V.Daggett, and A.R.Fersht (2000).
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation.
  Proc Natl Acad Sci U S A, 97, 13518-13522.  
10813836 V.Nanda, and L.Brand (2000).
Aromatic interactions in homeodomains contribute to the low quantum yield of a conserved, buried tryptophan.
  Proteins, 40, 112-125.  
10052460 D.E.Piper, A.H.Batchelor, C.P.Chang, M.L.Cleary, and C.Wolberger (1999).
Structure of a HoxB1-Pbx1 heterodimer bound to DNA: role of the hexapeptide and a fourth homeodomain helix in complex formation.
  Cell, 96, 587-597.
PDB code: 1b72
9552160 F.Avbelj, and L.Fele (1998).
Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation.
  Proteins, 31, 74-96.  
9565750 J.P.Schneider, A.Lombardi, and W.F.DeGrado (1998).
Analysis and design of three-stranded coiled coils and three-helix bundles.
  Fold Des, 3, R29-R40.  
8696974 C.Wolberger (1996).
Homeodomain interactions.
  Curr Opin Struct Biol, 6, 62-68.  
  8557047 J.A.Hirsch, and A.K.Aggarwal (1995).
Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.
  EMBO J, 14, 6280-6291.
PDB code: 1jgg
  8563623 N.D.Clarke (1995).
Covariation of residues in the homeodomain sequence family.
  Protein Sci, 4, 2269-2278.  
7579658 N.D.Clarke (1995).
Sequence 'minimization': exploring the sequence landscape with simplified sequences.
  Curr Opin Biotechnol, 6, 467-472.  
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.