PDBsum entry 1cty

Electron transport (heme protein)

PDB id

1cty

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Contents

			Protein chain

					108 a.a. *

			Ligands

					SO4


					HEC

			Waters ×30

* Residue conservation analysis

PDB id:

1cty

Links

Name:

Electron transport (heme protein)

Title:

Mutation of tyrosine-67 in cytochromE C significantly alters the local heme environment

Structure:

CytochromE C. Chain: a. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932

Resolution:

2.20Å

R-factor:

0.196

Authors:

A.M.Berghuis,G.D.Brayer

Key ref:

A.M.Berghuis et al. (1994). Mutation of tyrosine-67 to phenylalanine in cytochrome c significantly alters the local heme environment. J Mol Biol, 235, 1326-1341. PubMed id: 8308895

Date:

15-Feb-93

Release date:

15-Jul-93

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 3 residue positions (black crosses)

	J Mol Biol 235:1326-1341 (1994)
PubMed id: 8308895

Mutation of tyrosine-67 to phenylalanine in cytochrome c significantly alters the local heme environment.
A.M.Berghuis, J.G.Guillemette, M.Smith, G.D.Brayer.

ABSTRACT

The high resolution three-dimensional atomic structures of the reduced and oxidized states of the Y67F variant of yeast iso-1-cytochrome c have been completed. The conformational differences observed are localized directly in the mutation site and in the region about the pyrrole A propionate. Shifts in atomic positions are largely restricted to nearby amino acid side-chains, whereas little perturbation of the polypeptide chain backbone is observed. One prominent difference between the variant and wild-type structures involves a substantial increase in the size of an already existing internal cavity adjacent to residue 67. This same cavity contains an internally bound water molecule (Wat166), which is found in all eukaryotic cytochromes c for which structures are available. In the reduced Y67F mutant protein a second water molecule (Wat300) is observed to reside in this enlarged internal cavity, assuming a position approximately equivalent to that of the hydroxyl group of Tyr67 in the wild-type protein. A further consequence of this mutation is the alteration of the hydrogen bond network between Tyr67, Wat166 and other nearby residues. This appears to be responsible for the absence of oxidation state dependent changes in polypeptide chain flexibility observed in the wild-type protein. Furthermore, loss of the normally resident Tyr67 OH to Met80 SD hydrogen bond leads to a significantly lower midpoint reduction potential. These results reaffirm proposals that both Tyr67 and Wat166 play a central role in stabilizing the alternative oxidation states of cytochrome c.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20238133

F.Sinibaldi, B.D.Howes, M.C.Piro, F.Polticelli, C.Bombelli, T.Ferri, M.Coletta, G.Smulevich, and R.Santucci (2010).
Extended cardiolipin anchorage to cytochrome c: a model for protein-mitochondrial membrane binding.

J Biol Inorg Chem, 15, 689-700.

18974097

L.A.Abriata, A.Cassina, V.Tórtora, M.Marín, J.M.Souza, L.Castro, A.J.Vila, and R.Radi (2009).
Nitration of solvent-exposed tyrosine 74 on cytochrome c triggers heme iron-methionine 80 bond disruption. Nuclear magnetic resonance and optical spectroscopy studies.

J Biol Chem, 284, 17-26.

19617967

T.Ying, Z.H.Wang, Y.W.Lin, J.Xie, X.Tan, and Z.X.Huang (2009).
Tyrosine-67 in cytochrome c is a possible apoptotic trigger controlled by hydrogen bonds via a conformational transition.

Chem Commun (Camb), (), 4512-4514.

18947229

G.Zoppellaro, E.Harbitz, R.Kaur, A.A.Ensign, K.L.Bren, and K.K.Andersson (2008).
Modulation of the ligand-field anisotropy in a series of ferric low-spin cytochrome c mutants derived from Pseudomonas aeruginosa cytochrome c-551 and Nitrosomonas europaea cytochrome c-552: a nuclear magnetic resonance and electron paramagnetic resonance study.

J Am Chem Soc, 130, 15348-15360.

16320010

F.Sinibaldi, B.D.Howes, M.C.Piro, P.Caroppi, G.Mei, F.Ascoli, G.Smulevich, and R.Santucci (2006).
Insights into the role of the histidines in the structure and stability of cytochrome c.

J Biol Inorg Chem, 11, 52-62.

12042067

M.Paoli, J.Marles-Wright, and A.Smith (2002).
Structure-function relationships in heme-proteins.

DNA Cell Biol, 21, 271-280.

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

11502215

F.Sinibaldi, L.Fiorucci, G.Mei, T.Ferri, A.Desideri, F.Ascoli, and R.Santucci (2001).
Cytochrome c reconstituted from two peptide fragments displays native-like redox properties.

Eur J Biochem, 268, 4537-4543.

11027143

R.Santucci, C.Bongiovanni, G.Mei, T.Ferri, F.Polizio, and A.Desideri (2000).
Anion size modulates the structure of the A state of cytochrome c.

Biochemistry, 39, 12632-12638.

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.

10386873

J.Read, R.Gill, S.L.Dales, J.B.Cooper, S.P.Wood, and C.Anthony (1999).
The molecular structure of an unusual cytochrome c2 determined at 2.0 A; the cytochrome cH from Methylobacterium extorquens.

Protein Sci, 8, 1232-1240.

PDB code:

1qn2

9622485

C.Sebban-Kreuzer, M.Blackledge, A.Dolla, D.Marion, and F.Guerlesquin (1998).
Tyrosine 64 of cytochrome c553 is required for electron exchange with formate dehydrogenase in Desulfovibrio vulgaris Hildenborough.

Biochemistry, 37, 8331-8340.

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.

9568906

J.S.Fetrow, U.Dreher, D.J.Wiland, D.L.Schaak, and T.L.Boose (1998).
Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c.

Protein Sci, 7, 994.

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.

9007992

J.S.Fetrow, S.R.Horner, W.Oehrl, D.L.Schaak, T.L.Boose, and R.E.Burton (1997).
Analysis of the structure and stability of omega loop A replacements in yeast iso-1-cytochrome c.

Protein Sci, 6, 197-210.

9062118

K.Qu, J.L.Vaughn, A.Sienkiewicz, C.P.Scholes, and J.S.Fetrow (1997).
Kinetics and motional dynamics of spin-labeled yeast iso-1-cytochrome c: 1. Stopped-flow electron paramagnetic resonance as a probe for protein folding/unfolding of the C-terminal helix spin-labeled at cysteine 102.

Biochemistry, 36, 2884-2897.

9144797

P.Haney, J.Konisky, K.K.Koretke, Z.Luthey-Schulten, and P.G.Wolynes (1997).
Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus.

Proteins, 28, 117-130.

9154933

S.Othman, J.Fitch, M.A.Cusanovich, and A.Desbois (1997).
Influence of conserved amino acids on the structure and environment of the heme of cytochrome c2. A resonance Raman study.

Biochemistry, 36, 5499-5508.

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.

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

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.