spacer
spacer

PDBsum entry 451c
Go to PDB code: 
protein ligands links
Electron transport PDB id
451c

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
82 a.a. *
Ligands
HEM
Waters ×73
* Residue conservation analysis
PDB id:
451c
Name: Electron transport
Title: Structure of cytochrome c551 from p. Aeruginosa refined at 1.6 angstroms resolution and comparison of the two redox forms
Structure: Cytochrome c551. Chain: a. Engineered: yes
Source: Pseudomonas aeruginosa. Organism_taxid: 287
Resolution:
1.60Å     R-factor:   0.187    
Authors: Y.Matsuura,T.Takano,R.E.Dickerson
Key ref:
Y.Matsuura et al. (1982). Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms. J Mol Biol, 156, 389-409. PubMed id: 6283101 DOI: 10.1016/0022-2836(82)90335-7
Date:
20-Jul-81     Release date:   02-Oct-81    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00099  (CY551_PSEAE) -  Cytochrome c-551 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Seq:
Struc: 		104 a.a.
82 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/0022-2836(82)90335-7 J Mol Biol 156:389-409 (1982)
PubMed id: 6283101  
 
 
Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms.
Y.Matsuura, T.Takano, R.E.Dickerson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 3.
FIG. 3. All theside-chains onan a-carbon skeleton. (a) Front view, and (b) view from Met61 aide. Not.e a long sequence of hydrophobic residues along the edge of heme crevice on the Met61 side. 		Figure 9.
FIG. 9. Hydrogen-bod network among water molecules (WAT) 11. 23 and 25. LyslOCO Ile48CO. ro62C0, sn64Nd and 06 MetGlS, and Ala65NH in the heme crevice of the reduced frm. Probable ydrogens are indicated by thick lines on hydrogen bonds. Circles adjacent to water molecules 23 ad 25 indicate their positions in the oxidized form.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1982, 156, 389-409) copyright 1982.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22266822 Y.Matsumoto, T.Tosha, A.V.Pisliakov, T.Hino, H.Sugimoto, S.Nagano, Y.Sugita, and Y.Shiro (2012).
Crystal structure of quinol-dependent nitric oxide reductase from Geobacillus stearothermophilus.
  Nat Struct Mol Biol, 19, 238-245.
PDB codes: 3ayf 3ayg
20014790 J.D.Martell, H.Li, T.Doukov, P.Martásek, L.J.Roman, M.Soltis, T.L.Poulos, and R.B.Silverman (2010).
Heme-coordinating inhibitors of neuronal nitric oxide synthase. Iron-thioether coordination is stabilized by hydrophobic contacts without increased inhibitor potency.
  J Am Chem Soc, 132, 798-806.
PDB codes: 3jt3 3jt4 3jt5 3jt6 3jt7 3jt8 3jt9 3jta
19536822 G.Zoppellaro, K.L.Bren, A.A.Ensign, E.Harbitz, R.Kaur, H.P.Hersleth, U.Ryde, L.Hederstedt, and K.K.Andersson (2009).
Review: studies of ferric heme proteins with highly anisotropic/highly axial low spin (S = 1/2) electron paramagnetic resonance signals with bis-histidine and histidine-methionine axial iron coordination.
  Biopolymers, 91, 1064-1082.  
19294434 S.J.Takayama, K.Irie, H.Tai, T.Kawahara, S.Hirota, T.Takabe, L.A.Alcaraz, A.Donaire, and Y.Yamamoto (2009).
Electron transfer from cytochrome c to cupredoxins.
  J Biol Inorg Chem, 14, 821-828.  
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.  
18392863 L.V.Michel, and K.L.Bren (2008).
Submolecular unfolding units of Pseudomonas aeruginosa cytochrome c-551.
  J Biol Inorg Chem, 13, 837-845.  
17407190 A.R.Bizzarri, E.Brunori, B.Bonanni, and S.Cannistraro (2007).
Docking and molecular dynamics simulation of the Azurin-Cytochrome c551 electron transfer complex.
  J Mol Recognit, 20, 122-131.  
17513370 G.Zucchelli, D.Brogioli, A.P.Casazza, F.M.Garlaschi, and R.C.Jennings (2007).
Chlorophyll ring deformation modulates Qy electronic energy in chlorophyll-protein complexes and generates spectral forms.
  Biophys J, 93, 2240-2254.  
17900177 L.V.Michel, T.Ye, S.E.Bowman, B.D.Levin, M.A.Hahn, B.S.Russell, S.J.Elliott, and K.L.Bren (2007).
Heme attachment motif mobility tunes cytochrome c redox potential.
  Biochemistry, 46, 11753-11760.  
17496029 Q.Liang, G.T.Miller, C.A.Beeghley, C.B.Graf, and R.Timkovich (2007).
Solution conformation of the His-47 to Ala-47 mutant of Pseudomonas stutzeri ZoBell ferrocytochrome c-551.
  Biophys J, 93, 1700-1706.
PDB code: 2i8f
16452476 A.Borgia, D.Bonivento, C.Travaglini-Allocatelli, A.Di Matteo, and M.Brunori (2006).
Unveiling a hidden folding intermediate in c-type cytochromes by protein engineering.
  J Biol Chem, 281, 9331-9336.
PDB code: 2exv
15883159 C.Travaglini-Allocatelli, S.Gianni, V.K.Dubey, A.Borgia, A.Di Matteo, D.Bonivento, F.Cutruzzolà, K.L.Bren, and M.Brunori (2005).
An obligatory intermediate in the folding pathway of cytochrome c552 from Hydrogenobacter thermophilus.
  J Biol Chem, 280, 25729-25734.
PDB code: 1ynr
16310725 T.Goto, T.Matsuno, M.Hishinuma-Narisawa, K.Yamazaki, H.Matsuyama, N.Inoue, and I.Yumoto (2005).
Cytochrome c and bioenergetic hypothetical model for alkaliphilic Bacillus spp.
  J Biosci Bioeng, 100, 365-379.  
15155756 J.Alric, M.Yoshida, K.V.Nagashima, R.Hienerwadel, P.Parot, A.Verméglio, S.W.Chen, and J.L.Pellequer (2004).
Two distinct binding sites for high potential iron-sulfur protein and cytochrome c on the reaction center-bound cytochrome of Rubrivivax gelatinosus.
  J Biol Chem, 279, 32545-32553.  
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.  
12486716 M.A.Ceruso, A.Grottesi, and A.Di Nola (2003).
Dynamic effects of mutations within two loops of cytochrome c551 from Pseudomonas aeruginosa.
  Proteins, 50, 222-229.  
12022864 D.M.Tiede, R.Zhang, and S.Seifert (2002).
Protein conformations explored by difference high-angle solution X-ray scattering: oxidation state and temperature dependent changes in cytochrome C.
  Biochemistry, 41, 6605-6614.  
11168887 E.Bouchayer, C.I.Stassinopoulou, C.Tzougraki, D.Marion, and P.Gans (2001).
NMR and CD conformational studies of the C-terminal 16-peptides of Pseudomonas aeruginosa c551 and Hydrogenobacter thermophilus c552 cytochromes.
  J Pept Res, 57, 39-47.  
11371465 G.T.Miller, J.K.Hardman, and R.Timkovich (2001).
Solution conformation of the Met 61 to His 61 mutant of Pseudomonas stutzeri ZoBell ferrocytochrome c-551.
  Biophys J, 80, 2928-2934.
PDB code: 1fi3
11478889 M.R.Sawaya, D.W.Krogmann, A.Serag, K.K.Ho, T.O.Yeates, and C.A.Kerfeld (2001).
Structures of cytochrome c-549 and cytochrome c6 from the cyanobacterium Arthrospira maxima.
  Biochemistry, 40, 9215-9225.
PDB codes: 1f1c 1f1f 1f1i 1f1y
11133964 M.Santana, M.M.Pereira, N.P.Elias, C.M.Soares, and M.Teixeira (2001).
Gene cluster of Rhodothermus marinus high-potential iron-sulfur Protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases.
  J Bacteriol, 183, 687-699.  
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
10450083 A.Amadei, M.A.Ceruso, and A.Di Nola (1999).
On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.
  Proteins, 36, 419-424.  
10196231 G.W.Pettigrew, S.Prazeres, C.Costa, N.Palma, L.Krippahl, I.Moura, and J.J.Moura (1999).
The structure of an electron transfer complex containing a cytochrome c and a peroxidase.
  J Biol Chem, 274, 11383-11389.  
10608805 J.Hasegawa, H.Shimahara, M.Mizutani, S.Uchiyama, H.Arai, M.Ishii, Y.Kobayashi, S.J.Ferguson, Y.Sambongi, and Y.Igarashi (1999).
Stabilization of Pseudomonas aeruginosa cytochrome c(551) by systematic amino acid substitutions based on the structure of thermophilic Hydrogenobacter thermophilus cytochrome c(552).
  J Biol Chem, 274, 37533-37537.  
9657676 J.Hasegawa, T.Yoshida, T.Yamazaki, Y.Sambongi, Y.Yu, Y.Igarashi, T.Kodama, K.Yamazaki, Y.Kyogoku, and Y.Kobayashi (1998).
Solution structure of thermostable cytochrome c-552 from Hydrogenobacter thermophilus determined by 1H-NMR spectroscopy.
  Biochemistry, 37, 9641-9649.
PDB code: 1ayg
9558336 K.Klarskov, G.Van Driessche, K.Backers, C.Dumortier, T.E.Meyer, G.Tollin, M.A.Cusanovich, and J.J.Van Beeumen (1998).
Ligand binding and covalent structure of an oxygen-binding heme protein from Rhodobacter sphaeroides, a representative of a new structural family of c-type cytochromes.
  Biochemistry, 37, 5995-6002.  
9746537 R.Timkovich, D.Bergmann, D.M.Arciero, and A.B.Hooper (1998).
Primary sequence and solution conformation of ferrocytochrome c-552 from Nitrosomonas europaea.
  Biophys J, 75, 1964-1972.
PDB codes: 1a56 1a8c
9533688 W.Jentzen, J.G.Ma, and J.A.Shelnutt (1998).
Conservation of the conformation of the porphyrin macrocycle in hemoproteins.
  Biophys J, 74, 753-763.  
9032080 A.Kadziola, and S.Larsen (1997).
Crystal structure of the dihaem cytochrome c4 from Pseudomonas stutzeri determined at 2.2A resolution.
  Structure, 5, 203-216.
PDB code: 1etp
9331415 D.Nurizzo, M.C.Silvestrini, M.Mathieu, F.Cutruzzolà, D.Bourgeois, V.Fülöp, J.Hajdu, M.Brunori, M.Tegoni, and C.Cambillau (1997).
N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
  Structure, 5, 1157-1171.
PDB code: 1nir
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.  
  9409151 W.G.Zumft (1997).
Cell biology and molecular basis of denitrification.
  Microbiol Mol Biol Rev, 61, 533-616.  
9201942 W.Hu, G.Van Driessche, B.Devreese, C.F.Goodhew, D.F.McGinnity, N.Saunders, V.Fulop, G.W.Pettigrew, and J.J.Van Beeumen (1997).
Structural characterization of Paracoccus denitrificans cytochrome c peroxidase and assignment of the low and high potential heme sites.
  Biochemistry, 36, 7958-7966.  
8612646 B.Samyn, L.De Smet, G.Van Driessche, T.E.Meyer, R.G.Bartsch, M.A.Cusanovich, and J.J.Van Beeumen (1996).
A high-potential soluble cytochrome c-551 from the purple phototrophic bacterium Chromatium vinosum is homologous to cytochrome c8 from denitrifying pseudomonads.
  Eur J Biochem, 236, 689-696.  
8621494 P.Mulligan-Pullyblank, J.S.Spitzer, B.M.Gilden, and J.S.Fetrow (1996).
Loop replacement and random mutagenesis of omega-loop D, residues 70-84, in iso-1-cytochrome c.
  J Biol Chem, 271, 8633-8645.  
8636074 X.Wang, M.E.Dumont, and F.Sherman (1996).
Sequence requirements for mitochondrial import of yeast cytochrome c.
  J Biol Chem, 271, 6594-6604.  
7851392 B.Bersch, B.Brutscher, T.E.Meyer, and D.Marion (1995).
1H and 13C NMR assignments and structural aspects of a ferrocytochrome c-551 from the purple phototrophic bacterium Ectothiorhodospira halophila.
  Eur J Biochem, 227, 249-260.  
7867644 D.L.Turner (1995).
Determination of haem electronic structure in His-Met cytochromes c by 13C-NMR. The effect of the axial ligands.
  Eur J Biochem, 227, 829-837.  
7779259 J.D.Hobbs, and J.A.Shelnutt (1995).
Conserved nonplanar heme distortions in cytochromes c.
  J Protein Chem, 14, 19-25.  
7767224 T.Fujiwara, T.Yamanaka, and Y.Fukumori (1995).
The amino acid sequence of Nitrosomonas europaea cytochrome c-552.
  Curr Microbiol, 31, 1-4.  
8055954 H.S.Costa, H.Santos, and D.L.Turner (1994).
An unusual conformation of the methionine haem ligand in cytochrome cL established by two-dimensional 1H-NMR.
  Eur J Biochem, 223, 783-789.  
8307031 L.Banci, I.Bertini, M.T.Cambria, F.Capozzi, and A.Dikiy (1994).
1H one-dimensional and two-dimensional NMR studies of the ferricytochrome c 551 from Rhodocyclus gelatinosus.
  Eur J Biochem, 219, 663-669.  
7957244 R.Timkovich, M.Cai, B.Zhang, D.M.Arciero, and A.B.Hooper (1994).
Characteristics of the paramagnetic 1H-NMR spectra of the ferricytochrome c-551 family.
  Eur J Biochem, 226, 159-168.  
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
8394812 H.S.Costa, H.Santos, and D.L.Turner (1993).
Characterization of the haem environment in Methylophilus methylotrophus ferricytochrome c" by 1H-NMR.
  Eur J Biochem, 215, 817-824.  
  8382992 L.Chen, F.S.Mathews, V.L.Davidson, M.Tegoni, C.Rivetti, and G.L.Rossi (1993).
Preliminary crystal structure studies of a ternary electron transfer complex between a quinoprotein, a blue copper protein, and a c-type cytochrome.
  Protein Sci, 2, 147-154.  
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
1587359 A.V.Kajava (1992).
Left-handed topology of super-secondary structure formed by aligned alpha-helix and beta-hairpin.
  FEBS Lett, 302, 8.  
1327881 M.Cai, and R.Timkovich (1992).
Ionization of the heme propionate substituents in pseudomonad cytochromes c-551.
  FEBS Lett, 311, 213-216.  
1907667 J.Rose, and F.Eisenmenger (1991).
A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm.
  J Mol Evol, 32, 340-354.  
2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
2107323 M.S.Johnson, M.J.Sutcliffe, and T.L.Blundell (1990).
Molecular anatomy: phyletic relationships derived from three-dimensional structures of proteins.
  J Mol Evol, 30, 43-59.  
2174771 M.van de Kamp, M.C.Silvestrini, M.Brunori, J.Van Beeumen, F.C.Hali, and G.W.Canters (1990).
Involvement of the hydrophobic patch of azurin in the electron-transfer reactions with cytochrome C551 and nitrite reductase.
  Eur J Biochem, 194, 109-118.  
2550090 D.W.Dixon, X.Hong, and S.E.Woehler (1989).
Electrostatic and steric control of electron self-exchange in cytochromes c, c551, and b5.
  Biophys J, 56, 339-351.  
2560195 J.S.Fetrow, T.S.Cardillo, and F.Sherman (1989).
Deletions and replacements of omega loops in yeast iso-1-cytochrome c.
  Proteins, 6, 372-381.  
  3709526 C.Chothia, and A.M.Lesk (1986).
The relation between the divergence of sequence and structure in proteins.
  EMBO J, 5, 823-826.  
3012528 G.Tollin, L.K.Hanson, M.Caffrey, T.E.Meyer, and M.A.Cusanovich (1986).
Redox pathways in electron-transfer proteins: correlations between reactivities, solvent exposure, and unpaired-spin-density distributions.
  Proc Natl Acad Sci U S A, 83, 3693-3697.  
3006116 H.Senn, and K.Wüthrich (1985).
Amino acid sequence, haem-iron co-ordination geometry and functional properties of mitochondrial and bacterial c-type cytochromes.
  Q Rev Biophys, 18, 111-134.  
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.

 

spacer
spacer