PDBsum entry 1f9c

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Isomerase PDB id
Protein chains
360 a.a. *
_MN ×2
Waters ×195
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of mle d178n variant
Structure: Protein (muconate cycloisomerase i). Chain: a, b. Synonym: cis,cis-muconate lactonizing enzyme i, mle. Engineered: yes. Mutation: yes
Source: Pseudomonas putida. Organism_taxid: 303. Strain: prs2000. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
2.50Å     R-factor:   0.187     R-free:   0.234
Authors: T.Kajander,L.Lehtio,P.C.Kahn,A.Goldman
Key ref:
T.Kajander et al. (2000). Buried charged surface in proteins. Structure, 8, 1203-1214. PubMed id: 11080642 DOI: 10.1016/S0969-2126(00)00520-7
10-Jul-00     Release date:   07-Mar-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q51958  (Q51958_PSEPU) -  Muconate lactonizing enzyme
373 a.a.
360 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1016/S0969-2126(00)00520-7 Structure 8:1203-1214 (2000)
PubMed id: 11080642  
Buried charged surface in proteins.
T.Kajander, P.C.Kahn, S.H.Passila, D.C.Cohen, L.Lehtiö, W.Adolfsen, J.Warwicker, U.Schell, A.Goldman.
BACKGROUND: The traditional picture of charged amino acids in globular proteins is that they are almost exclusively on the outside exposed to the solvent. Buried charges, when they do occur, are assumed to play an essential role in catalysis and ligand binding, or in stabilizing structure as, for instance, helix caps. RESULTS: By analyzing the amount and distribution of buried charged surface and charges in proteins over a broad range of protein sizes, we show that buried charge is much more common than is generally believed. We also show that the amount of buried charge rises with protein size in a manner which differs from other types of surfaces, especially aromatic and polar uncharged surfaces. In large proteins such as hemocyanin, 35% of all charges are greater than 75% buried. Furthermore, at all sizes few charged groups are fully exposed. As an experimental test, we show that replacement of the buried D178 of muconate lactonizing enzyme by N stabilizes the enzyme by 4.2 degrees C without any change in crystallographic structure. In addition, free energy calculations of stability support the experimental results. CONCLUSIONS: Nature may use charge burial to reduce protein stability; not all buried charges are fully stabilized by a prearranged protein environment. Consistent with this view, thermophilic proteins often have less buried charge. Modifying the amount of buried charge at carefully chosen sites may thus provide a general route for changing the thermophilicity or psychrophilicity of proteins.
  Selected figure(s)  
Figure 4.
Figure 4. The Structures of the Regions Containing D178, H181, and D150 in Wild-Type MLE and the D178N VariantWild type, (a); Di78N, (b). The path of the backbone is shown as a "worm." D178, H151, and D150, as well as residues that interact with them, are in ball and stick. Oxygen is red; nitrogen is blue. Hydrogen bonds are shown as dotted lines. The figure was prepared using MOLSCRIPT [65] and Raster3D [66]

  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1203-1214) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377472 C.N.Pace, H.Fu, K.L.Fryar, J.Landua, S.R.Trevino, B.A.Shirley, M.M.Hendricks, S.Iimura, K.Gajiwala, J.M.Scholtz, and G.R.Grimsley (2011).
Contribution of hydrophobic interactions to protein stability.
  J Mol Biol, 408, 514-528.  
20838850 G.López, A.Bañares-Hidalgo, and P.Estrada (2011).
Xylanase II from Trichoderma reesei QM 9414: conformational and catalytic stability to Chaotropes, Trifluoroethanol, and pH changes.
  J Ind Microbiol Biotechnol, 38, 113-125.  
20195530 Groot, and S.Ventura (2010).
Protein aggregation profile of the bacterial cytosol.
  PLoS One, 5, e9383.  
  19177365 M.Sagermann, R.R.Chapleau, E.DeLorimier, and M.Lei (2009).
Using affinity chromatography to engineer and characterize pH-dependent protein switches.
  Protein Sci, 18, 217-228.
PDB codes: 3crt 3cru 3d0z
19004768 D.G.Isom, B.R.Cannon, C.A.Castañeda, A.Robinson, and B.García-Moreno (2008).
High tolerance for ionizable residues in the hydrophobic interior of proteins.
  Proc Natl Acad Sci U S A, 105, 17784-17788.  
18369193 M.J.Harms, J.L.Schlessman, M.S.Chimenti, G.R.Sue, A.Damjanović, and B.García-Moreno (2008).
A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values.
  Protein Sci, 17, 833-845.
PDB code: 2rks
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
16551626 L.J.Falomir-Lockhart, L.Laborde, P.C.Kahn, J.Storch, and B.Córsico (2006).
Protein-membrane interaction and fatty acid transfer from intestinal fatty acid-binding protein to membranes. Support for a multistep process.
  J Biol Chem, 281, 13979-13989.  
16905113 M.R.Gunner, J.Mao, Y.Song, and J.Kim (2006).
Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.
  Biochim Biophys Acta, 1757, 942-968.  
15306378 C.N.Pace, S.Treviño, E.Prabhakaran, and J.M.Scholtz (2004).
Protein structure, stability and solubility in water and other solvents.
  Philos Trans R Soc Lond B Biol Sci, 359, 1225.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
15340924 K.B.Murray, W.R.Taylor, and J.M.Thornton (2004).
Toward the detection and validation of repeats in protein structure.
  Proteins, 57, 365-380.  
14500895 G.I.Yakovlev, V.A.Mitkevich, K.L.Shaw, S.Trevino, S.Newsom, C.N.Pace, and A.A.Makarov (2003).
Contribution of active site residues to the activity and thermal stability of ribonuclease Sa.
  Protein Sci, 12, 2367-2373.  
14635121 S.Balaji, S.Aruna, and N.Srinivasan (2003).
Tolerance to the substitution of buried apolar residues by charged residues in the homologous protein structures.
  Proteins, 53, 783-791.  
12930985 T.Kajander, L.Lehtiö, M.Schlömann, and A.Goldman (2003).
The structure of Pseudomonas P51 Cl-muconate lactonizing enzyme: co-evolution of structure and dynamics with the dehalogenation function.
  Protein Sci, 12, 1855-1864.
PDB code: 1nu5
12543706 T.V.Chalikian (2003).
Volumetric properties of proteins.
  Annu Rev Biophys Biomol Struct, 32, 207-235.  
14648760 T.V.Chalikian (2003).
Hydrophobic tendencies of polar groups as a major force in molecular recognition.
  Biopolymers, 70, 492-496.  
11796115 C.W.Levy, P.A.Buckley, S.Sedelnikova, Y.Kato, Y.Asano, D.W.Rice, and P.J.Baker (2002).
Insights into enzyme evolution revealed by the structure of methylaspartate ammonia lyase.
  Structure, 10, 105-113.
PDB codes: 1kko 1kkr
12403817 I.M.Skerrett, J.Aronowitz, J.H.Shin, G.Cymes, E.Kasperek, F.L.Cao, and B.J.Nicholson (2002).
Identification of amino acid residues lining the pore of a gap junction channel.
  J Cell Biol, 159, 349-360.  
12119041 N.Mitra, V.R.Srinivas, T.N.Ramya, N.Ahmad, G.B.Reddy, and A.Surolia (2002).
Conformational stability of legume lectins reflect their different modes of quaternary association: solvent denaturation studies on concanavalin A and winged bean acidic agglutinin.
  Biochemistry, 41, 9256-9263.  
11863438 P.Phelan, A.A.Gorfe, I.Jelesarov, D.N.Marti, J.Warwicker, and H.R.Bosshard (2002).
Salt bridges destabilize a leucine zipper designed for maximized ion pairing between helices.
  Biochemistry, 41, 2998-3008.  
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.