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PDBsum entry 1ieu

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protein links
Electron transport PDB id
1ieu
Jmol
Contents
Protein chain
94 a.a. *
* Residue conservation analysis
PDB id:
1ieu
Name: Electron transport
Title: Apocytochrome b5, ph 6.2, 298 k, nmr, 10 structures
Structure: Apocytochrome b5. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Cell_line: bl21. Organ: liver. Gene: cytb5. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: C.J.Falzone,J.T.J.Lecomte
Key ref:
C.J.Falzone et al. (1996). Design challenges for hemoproteins: the solution structure of apocytochrome b5. Biochemistry, 35, 6519-6526. PubMed id: 8639599 DOI: 10.1021/bi960501q
Date:
20-Apr-96     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00173  (CYB5_RAT) -  Cytochrome b5
Seq:
Struc:
134 a.a.
94 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     heme binding     1 term  

 

 
DOI no: 10.1021/bi960501q Biochemistry 35:6519-6526 (1996)
PubMed id: 8639599  
 
 
Design challenges for hemoproteins: the solution structure of apocytochrome b5.
C.J.Falzone, M.R.Mayer, E.L.Whiteman, C.D.Moore, J.T.Lecomte.
 
  ABSTRACT  
 
In order to characterize the structural and dynamic factors that determine the assembly in b hemoproteins, the solution structure of the 98-residue protein apocytochrome b5 was determined by NMR methods. Over 800 experimental restraints derived from a series of two- and three-dimensional experiments were used. Holocytochrome b5, the protein with iron protoporphyrin-IX liganded to His-39 and His-63, contains in sequence the following elements of secondary structure: beta 1-alpha 1-beta 4-beta 3-alpha 2-alpha 3-beta 5-alpha 4-alpha 5-beta 2-alpha 6 [Mathews, F.S., Czerwinski, E. W., & Argos, P. (1979) The Porphyrins, Vol. 7, pp. 107-147, Academic Press, New York]. The folded holoprotein possesses two hydrophobic cores: an extensive, functional core around the heme (core 1), and a smaller, structural core remote from the heme (core 2). The apoprotein was found to contain a stable four-stranded beta-sheet encompassing beta 1, beta 2, beta 3, and beta 4 and three alpha-helices, corresponding to alpha 1, alpha 2, and alpha 6. Two short alpha-helices (alpha 3 and alpha 5) appear to form partially, and alpha 4 is not detected. These three helices and beta 5 border the heme binding pocket and are disordered in the apoprotein NMR structure. According to backbone 1H-15N NOE results, the most flexible region of the apoprotein, except for the termini, extends from Ala-50 (in beta 5) to Glu-69 (in alpha 5). The polypeptide segment bearing His-63 (located immediately prior to alpha 5) exhibits faster internal motions than that bearing His-39 (at the C-terminal end of alpha 2). The latter imidazole samples a restricted region of space, whereas the former can adopt many orientations with respect to the stable core. It was concluded that heme removal affects the structure and dynamics of most of core 1 whereas it leaves core 2 largely intact. The results provide guidelines for the rational design of b hemoproteins: a modular structure including a packed, stable core and a partially folded binding site is anticipated to present strong kinetic and thermodynamic advantages compared to approaches relying on the complete formation of secondary structure prior to heme binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20544970 L.J.Smith, A.Kahraman, and J.M.Thornton (2010).
Heme proteins--diversity in structural characteristics, function, and folding.
  Proteins, 78, 2349-2368.  
18041061 J.T.Lecomte, K.Mukhopadhyay, and M.P.Pond (2008).
Structural and thermodynamic encoding in the sequence of rat microsomal cytochrome b(5).
  Biopolymers, 89, 428-442.  
18398854 R.B.Davis, and J.T.Lecomte (2008).
Structural propensities in the heme binding region of apocytochrome b5. II. Heme conjugates.
  Biopolymers, 90, 556-566.  
18066653 Y.W.Lin, Z.H.Wang, F.Y.Ni, and Z.X.Huang (2008).
Forced unfolding of apocytochrome b5 by steered molecular dynamics simulation.
  Protein J, 27, 197-203.  
17456740 J.A.Knappenberger, and J.T.Lecomte (2007).
Loop anchor modification causes the population of an alternative native state in an SH3-like domain.
  Protein Sci, 16, 863-879.  
17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.
  Proteins, 68, 109-122.  
17299762 L.Wang, A.B.Cowley, S.Terzyan, X.Zhang, and D.R.Benson (2007).
Comparison of cytochromes b5 from insects and vertebrates.
  Proteins, 67, 293-304.
PDB code: 2ibj
17659366 S.D.Stojanović, V.B.Medaković, G.Predović, M.Beljanski, and S.D.Zarić (2007).
XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins.
  J Biol Inorg Chem, 12, 1063-1071.  
17153136 J.E.Bryant (2006).
In-cell protein dynamics.
  Mol Biosyst, 2, 406-410.  
15295112 A.B.Cowley, M.Rivera, and D.R.Benson (2004).
Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5.
  Protein Sci, 13, 2316-2329.  
15459337 J.A.Knappenberger, C.M.Kraemer-Pecore, and J.T.Lecomte (2004).
Insertion of the cytochrome b5 heme-binding loop into an SH3 domain. Effects on structure and stability, and clues about the cytochrome's architecture.
  Protein Sci, 13, 2899-2908.  
15152090 P.Picotti, A.Marabotti, A.Negro, V.Musi, B.Spolaore, M.Zambonin, and A.Fontana (2004).
Modulation of the structural integrity of helix F in apomyoglobin by single amino acid replacements.
  Protein Sci, 13, 1572-1585.  
12044160 M.Sugishima, H.Sakamoto, Y.Kakuta, Y.Omata, S.Hayashi, M.Noguchi, and K.Fukuyama (2002).
Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms.
  Biochemistry, 41, 7293-7300.
PDB code: 1irm
12199707 P.Yao, J.Wu, Y.H.Wang, B.Y.Sun, Z.X.Xia, and Z.X.Huang (2002).
X-ray crystallography, CD and kinetic studies revealed the essence of the abnormal behaviors of the cytochrome b5 Phe35-->Tyr mutant.
  Eur J Biochem, 269, 4287-4296.
PDB code: 1m20
11294656 C.J.Falzone, Y.Wang, B.C.Vu, N.L.Scott, S.Bhattacharya, and J.T.Lecomte (2001).
Structural and dynamic perturbations induced by heme binding in cytochrome b5.
  Biochemistry, 40, 4879-4891.
PDB codes: 1i87 1i8c
11371218 J.T.Lecomte, N.L.Scott, B.C.Vu, and C.J.Falzone (2001).
Binding of ferric heme by the recombinant globin from the cyanobacterium Synechocystis sp. PCC 6803.
  Biochemistry, 40, 6541-6552.  
11420436 V.V.Loladze, D.N.Ermolenko, and G.I.Makhatadze (2001).
Heat capacity changes upon burial of polar and nonpolar groups in proteins.
  Protein Sci, 10, 1343-1352.  
11266610 Z.Xu, and R.S.Farid (2001).
Design, synthesis, and characterization of a novel hemoprotein.
  Protein Sci, 10, 236-249.  
10821667 M.Ihara, S.Takahashi, K.Ishimori, and I.Morishima (2000).
Functions of fluctuation in the heme-binding loops of cytochrome b5 revealed in the process of heme incorporation.
  Biochemistry, 39, 5961-5970.  
10516571 E.Barbar (1999).
NMR characterization of partially folded and unfolded conformational ensembles of proteins.
  Biopolymers, 51, 191-207.  
10213608 E.M.Storch, V.Daggett, and W.M.Atkins (1999).
Engineering out motion: introduction of a de novo disulfide bond and a salt bridge designed to close a dynamic cleft on the surface of cytochrome b5.
  Biochemistry, 38, 5054-5064.  
  10422837 J.T.Lecomte, S.F.Sukits, S.Bhattacharya, and C.J.Falzone (1999).
Conformational properties of native sperm whale apomyoglobin in solution.
  Protein Sci, 8, 1484-1491.  
10029553 S.Bhattacharya, C.J.Falzone, and J.T.Lecomte (1999).
Backbone dynamics of apocytochrome b5 in its native, partially folded state.
  Biochemistry, 38, 2577-2589.  
10572010 S.Manyusa, G.Mortuza, and D.Whitford (1999).
Analysis of folding and unfolding reactions of cytochrome b5.
  Biochemistry, 38, 14352-14362.  
10625461 X.Kang, and J.Carey (1999).
Role of heme in structural organization of cytochrome c probed by semisynthesis.
  Biochemistry, 38, 15944-15951.  
  9761479 A.J.Constans, M.R.Mayer, S.F.Sukits, and J.T.Lecomte (1998).
A test of the relationship between sequence and structure in proteins: excision of the heme binding site in apocytochrome b5.
  Protein Sci, 7, 1983-1993.  
9708976 A.Perret, and D.Pompon (1998).
Electron shuttle between membrane-bound cytochrome P450 3A4 and b5 rules uncoupling mechanisms.
  Biochemistry, 37, 11412-11424.  
9521665 C.S.Miles, F.Lederer, and K.H.Lê (1998).
Probing intramolecular electron transfer within flavocytochrome b2 with a monoclonal antibody.
  Biochemistry, 37, 3440-3448.  
9521687 E.J.Fuentes, and A.J.Wand (1998).
Local dynamics and stability of apocytochrome b562 examined by hydrogen exchange.
  Biochemistry, 37, 3687-3698.  
9452426 R.J.Auchus, T.C.Lee, and W.L.Miller (1998).
Cytochrome b5 augments the 17,20-lyase activity of human P450c17 without direct electron transfer.
  J Biol Chem, 273, 3158-3165.  
  9300488 C.V.Gegg, K.E.Bowers, and C.R.Matthews (1997).
Probing minimal independent folding units in dihydrofolate reductase by molecular dissection.
  Protein Sci, 6, 1885-1892.  
9363779 L.Banci, I.Bertini, F.Ferroni, and A.Rosato (1997).
Solution structure of reduced microsomal rat cytochrome b5.
  Eur J Biochem, 249, 270-279.
PDB code: 1aqa
9188711 L.D.Gruenke, J.Sun, T.M.Loehr, and L.Waskell (1997).
Resonance Raman spectral properties and stability of manganese protoporphyrin IX cytochrome b5.
  Biochemistry, 36, 7114-7125.  
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 code is shown on the right.