PDBsum entry 1crh

Electron transport(cytochrome)

PDB id

1crh

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Contents

			Protein chain

					108 a.a. *

			Ligands

					SO4


					HEC

			Waters ×58

* Residue conservation analysis

PDB id:

1crh

Links

Name:

Electron transport(cytochrome)

Title:

The role of a conserved internal water molecule and its associated hydrogen bond network in cytochromE C

Structure:

CytochromE C. Chain: a. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: potential

Resolution:

1.90Å

R-factor:

0.185

Authors:

A.M.Berghuis,G.D.Brayer

Key ref:

A.M.Berghuis et al. (1994). The role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c. J Mol Biol, 236, 786-799. PubMed id: 8114094

Date:

06-Aug-93

Release date:

31-Jan-94

PROCHECK

	Headers

	References

Protein chain

P00044 (CYC1_YEAST) - Cytochrome c isoform 1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: Struc:					109 a.a. 108 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

	J Mol Biol 236:786-799 (1994)
PubMed id: 8114094

The role of a conserved internal water molecule and its associated hydrogen bond network in cytochrome c.
A.M.Berghuis, J.G.Guillemette, G.McLendon, F.Sherman, M.Smith, G.D.Brayer.

ABSTRACT

High resolution three-dimensional structures for the N52I and N52I-Y67F yeast iso-1-cytochrome c variants have been completed in both oxidation states. The most prominent structural difference observed in both mutant proteins is the displacement of a conserved, internally bound water molecule (Wat166) from the protein matrix. In wild-type yeast iso-1-cytochrome c the position and orientation of this water molecule is found to be dependent on the oxidation state of the heme iron atom. Overall our results suggest the function of Wat166 and its associated hydrogen bond network is threefold. First, the presence of Wat166 provides a convenient mechanism to modify the hydrogen bond network involving several residues near the Met80 ligand in an oxidation state dependent manner. Second, Wat166 is necessary for the maintenance of the spatial relationships between nearby side-chains and the hydrogen bond interactions formed between these groups in this region of the protein. An essential part of this role is ensuring the proper conformation of the side-chain of Tyr67 so that it forms a hydrogen bond interaction with the heme ligand Met80. This hydrogen bond influences the electron withdrawing power of the Met80 ligand and is therefore a factor in controlling the midpoint reduction potential of cytochrome c. Elimination of this interaction in the N52I-Y67F mutant protein or elimination of Wat166 in the N52I protein with the subsequent disruption in the position and interactions of the Tyr67 side-chain, leads to a drop of approximately 56 mV in the observed midpoint reduction potential of the heme group. Third, Wat166 also appears to mediate increases in the mobility of three nearby segments of polypeptide chain when cytochrome c is in the oxidized state. Previous studies have proposed these changes may be related to oxidation state dependent interactions between cytochrome c and its redox partners. Coincident with the absence of Wat166, such mobility changes are not observed in the N52I and N52I-Y67F mutant proteins. It is possible that much of the increased protein stability observed for both mutant proteins may be due to this factor. Finally, our results show that neither heme iron charge nor heme plane distortion are responsible for oxidation state dependent conformational changes in the pyrrole A propionate region. Instead, the changes observed appear to be driven by the change in conformation that the side-chain of Asn52 experiences as the result of oxidation state dependent movement of Wat166.

Literature references that cite this PDB file's key reference

PubMed id

Reference

16700049

C.A.Bottoms, T.A.White, and J.J.Tanner (2006).
Exploring structurally conserved solvent sites in protein families.

Proteins, 64, 404-421.

15161973

L.Zhong, X.Wen, T.M.Rabinowitz, B.S.Russell, E.F.Karan, and K.L.Bren (2004).
Heme axial methionine fluxionality in Hydrogenobacter thermophilus cytochrome c552.

Proc Natl Acad Sci U S A, 101, 8637-8642.

11742117

S.Geremia, G.Garau, L.Vaccari, R.Sgarra, M.S.Viezzoli, M.Calligaris, and L.Randaccio (2002).
Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.

Protein Sci, 11, 6.

PDB codes:

1fj0 1i8o 1i8p

11566802

C.Blouin, J.G.Guillemette, and C.J.Wallace (2001).
Resolving the individual components of a pH-induced conformational change.

Biophys J, 81, 2331-2338.

11316887

J.Xu, W.A.Baase, M.L.Quillin, E.P.Baldwin, and B.W.Matthews (2001).
Structural and thermodynamic analysis of the binding of solvent at internal sites in T4 lysozyme.

Protein Sci, 10, 1067-1078.

PDB codes:

1g06 1g07 1g0g 1g0j 1g0k 1g0l 1g0m 1g0p 1g0q 1g1v 1g1w 1i6s

10956004

A.Maeda, F.L.Tomson, R.B.Gennis, H.Kandori, T.G.Ebrey, and S.P.Balashov (2000).
Relocation of internal bound water in bacteriorhodopsin during the photoreaction of M at low temperatures: an FTIR study.

Biochemistry, 39, 10154-10162.

10769113

D.H.Kim, D.S.Jang, G.H.Nam, G.Choi, J.S.Kim, N.C.Ha, M.S.Kim, B.H.Oh, and K.Y.Choi (2000).
Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.

Biochemistry, 39, 4581-4589.

PDB codes:

1dmm 1dmn 1dmq

11052663

S.Benini, A.González, W.R.Rypniewski, K.S.Wilson, J.J.Van Beeumen, and S.Ciurli (2000).
Crystal structure of oxidized Bacillus pasteurii cytochrome c553 at 0.97-A resolution.

Biochemistry, 39, 13115-13126.

PDB codes:

1b7v 1c75

11092924

S.Yamada, S.Y.Park, H.Shimizu, Y.Koshizuka, K.Kadokura, T.Satoh, K.Suruga, M.Ogawa, Y.Isogai, T.Nishio, Y.Shiro, and T.Oku (2000).
Structure of cytochrome c6 from the red alga Porphyra yezoensis at 1. 57 A resolution.

Acta Crystallogr D Biol Crystallogr, 56, 1577-1582.

PDB code:

1gdv

10209296

J.A.Kornblatt, M.J.Kornblatt, R.Lange, E.Mombelli, and J.G.Guillemette (1999).
The individual tyrosines of proteins: their spectra may or may not differ from those in water or other solvents.

Biochim Biophys Acta, 1431, 238-248.

9748230

C.Dumortier, J.M.Holt, T.E.Meyer, and M.A.Cusanovich (1998).
Imidazole binding to Rhodobacter capsulatus cytochrome c2. Effect of site-directed mutants on ligand binding.

J Biol Chem, 273, 25647-25653.

9545034

C.M.Soares, P.J.Martel, J.Mendes, and M.A.Carrondo (1998).
Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations.

Biophys J, 74, 1708-1721.

9512015

J.M.Ortega, B.Dohse, D.Oesterhelt, and P.Mathis (1998).
Low-temperature electron transfer from cytochrome to the special pair in Rhodopseudomonas viridis: role of the L162 residue.

Biophys J, 74, 1135-1148.

9485396

J.S.Fetrow, J.S.Spitzer, B.M.Gilden, S.J.Mellender, T.J.Begley, B.J.Haas, and T.L.Boose (1998).
Structure, function, and temperature sensitivity of directed, random mutants at proline 76 and glycine 77 in omega-loop D of yeast iso-1-cytochrome c.

Biochemistry, 37, 2477-2487.

9541406

J.S.Milne, L.Mayne, H.Roder, A.J.Wand, and S.W.Englander (1998).
Determinants of protein hydrogen exchange studied in equine cytochrome c.

Protein Sci, 7, 739-745.

9538000

L.Banci, I.Bertini, M.A.De la Rosa, D.Koulougliotis, J.A.Navarro, and O.Walter (1998).
Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.

Biochemistry, 37, 4831-4843.

PDB codes:

1a2s 1ced

9605312

W.A.McGee, and B.T.Nall (1998).
Refolding rate of stability-enhanced cytochrome c is independent of thermodynamic driving force.

Protein Sci, 7, 1071-1082.

9404638

H.R.Schroeder, F.A.McOdimba, J.G.Guillemette, and J.A.Kornblatt (1997).
The polarity of tyrosine 67 in yeast iso-1-cytochrome c monitored by second derivative spectroscopy.

Biochem Cell Biol, 75, 191-197.

9395318

L.Banci, G.Gori-Savellini, and P.Turano (1997).
A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states.

Eur J Biochem, 249, 716-723.

9220987

L.Banci, I.Bertini, K.L.Bren, H.B.Gray, P.Sompornpisut, and P.Turano (1997).
Solution structure of oxidized Saccharomyces cerevisiae iso-1-cytochrome c.

Biochemistry, 36, 8992-9001.

PDB code:

1yic

8910563

C.M.Lett, A.M.Berghuis, H.E.Frey, J.R.Lepock, and J.G.Guillemette (1996).
The role of a conserved water molecule in the redox-dependent thermal stability of iso-1-cytochrome c.

J Biol Chem, 271, 29088-29093.

8652517

D.F.Doyle, J.C.Waldner, S.Parikh, L.Alcazar-Roman, and G.J.Pielak (1996).
Changing the transition state for protein (Un) folding.

Biochemistry, 35, 7403-7411.

8611575

M.Hervás, J.A.Navarro, A.Díaz, and M.A.De la Rosa (1996).
A comparative thermodynamic analysis by laser-flash absorption spectroscopy of photosystem I reduction by plastocyanin and cytochrome c6 in Anabaena PCC 7119, Synechocystis PCC 6803 and Spinach.

Biochemistry, 35, 2693-2698.

8718869

S.P.Rafferty, J.G.Guillemette, A.M.Berghuis, M.Smith, G.D.Brayer, and A.G.Mauk (1996).
Mechanistic and structural contributions of critical surface and internal residues to cytochrome c electron transfer reactivity.

Biochemistry, 35, 10784-10792.

PDB codes:

1irv 1irw

8639684

W.A.McGee, F.I.Rosell, J.R.Liggins, S.Rodriguez-Ghidarpour, Y.Luo, J.Chen, G.D.Brayer, A.G.Mauk, and B.T.Nall (1996).
Thermodynamic cycles as probes of structure in unfolded proteins.

Biochemistry, 35, 1995-2007.

PDB code:

1ytc

8789192

C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.

J Comput Aided Mol Des, 9, 500-512.

8535241

P.Shih, D.R.Holland, and J.F.Kirsch (1995).
Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules.

Protein Sci, 4, 2050-2062.

PDB codes:

1lsm 1lsn

8033888

Y.Huang, S.Beeser, J.G.Guillemette, R.K.Storms, and J.A.Kornblatt (1994).
Mutations of iso-1-cytochrome c at positions 13 and 90. Separate effects on physical and functional properties.

Eur J Biochem, 223, 155-160.

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.