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PDBsum entry 1b5m
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Electron transport PDB id
1b5m

 

 

 

 

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Contents
Protein chain
84 a.a. *
Ligands
HEM
* Residue conservation analysis
PDB id:
1b5m
Name: Electron transport
Title: Rat outer mitochondrial membrane cytochrome b5
Structure: Cytochrome b5. Chain: a. Fragment: water soluble domain. Engineered: yes. Other_details: from rat outer mitochondrial membrane
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Cell_line: bl21. Organ: liver. Cell: hepatocyte. Organelle: mitochondrion. Cellular_location: outer mitochondrial membrane. Expressed in: escherichia coli bl21(de3).
Resolution:
2.70Å     R-factor:   0.220    
Authors: M.Rivera,S.P.White,X.Zhang
Key ref:
M.J.Rodríguez-Marañón et al. (1996). 13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c. Biochemistry, 35, 16378-16390. PubMed id: 8973214 DOI: 10.1021/bi961895o
Date:
07-Nov-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P04166  (CYB5B_RAT) -  Cytochrome b5 type B from Rattus norvegicus
Seq:
Struc: 		146 a.a.
84 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi961895o Biochemistry 35:16378-16390 (1996)
PubMed id: 8973214  
 
 
13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c.
M.J.Rodríguez-Marañón, F.Qiu, R.E.Stark, S.P.White, X.Zhang, S.I.Foundling, V.Rodríguez, C.L.Schilling, R.A.Bunce, M.Rivera.
 
  ABSTRACT  
 
The role played by the outer mitochondrial membrane (OM) cytochrome b5 heme propionate groups in the electrostatic binding between OM cytochrome b5 and horse heart cytochrome c was investigated by 13C NMR spectroscopy and X-ray crystallography. To achieve these aims, 13C-labeled heme OM cytochrome b5 was expressed in Escherichia coli as previously described [Rivera M., Walker, F.A. (1995) Anal. Biochem. 230, 295-302]. Assignment of the resonances arising from the heme propionate carbons in ferricytochrome b5 was carried out by a combination of one- and two-dimensional NMR experiments. Titrations of [13C]heme-labeled OM cytochrome b5 with horse heart cytochrome c were carried out in order to monitor the resonances arising from the heme propionate carbonyl carbons in OM cytochrome b5. The results from these titrations clearly show that only the heme propionate located on the exposed heme edge in OM cytochrome b5 participates in the electrostatic stabilization of the complex between OM cytochrome b5 and horse heart cytochrome c. Similar experiments carried out monitoring 13C resonances arising from several other heme substituents demonstrated that the stoichiometry of the complex is 1:1. A conditional binding constant, K which equals 3.8 x 10(4) +/- 1.4 x 10(4) at mu = 0.02 M, was obtained for the formation of the complex by fitting the binding curves obtained experimentally to a model based on this stoichiometry. The X-ray crystal structure of rat liver OM cytochrome b5 solved to 2.7 A resolution shows that the structures of bovine liver microsomal cytochrome b5 and rat liver OM cytochrome b5 are almost identical when compared at medium resolution. The similarity between the two structures, combined with the findings that only the heme propionate located on the exposed heme edge of OM cytochrome b5 participates in the electrostatic binding to cytochrome c and that the stability of this complex is similar to that measured for the association between microsomal cytochrome b5 and cytochrome c, clearly indicates that the site of interaction on OM cytochrome b5 is almost identical to the one elucidated for microsomal cytochrome b5. It is therefore possible to conclude that the large body of information gathered by many investigators for the nonphysiological interaction between microsomal cytochrome b5 and cytochrome c (recently reviewed) [Mauk, A. G. Mauk, M. R., Moore, G. R., & Northrup, S. H. (1995) Bioenerg. Biomembr. 27, 311-330] has indeed biological as well as pedagogical validity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20883776 C.R.Myers, W.E.Antholine, and J.M.Myers (2010).
The pro-oxidant chromium(VI) inhibits mitochondrial complex I, complex II, and aconitase in the bronchial epithelium: EPR markers for Fe-S proteins.
  Free Radic Biol Med, 49, 1903-1915.  
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
16308882 D.Paul, H.Miyake, S.Shinoda, and H.Tsukube (2006).
Proteo-dendrimers designed for complementary recognition of cytochrome c: dendrimer architecture toward nanoscale protein complexation.
  Chemistry, 12, 1328-1338.  
16807901 Q.Cheng, D.R.Benson, M.Rivera, and K.Kuczera (2006).
Influence of point mutations on the flexibility of cytochrome b5: molecular dynamics simulations of holoproteins.
  Biopolymers, 83, 297-312.  
15689516 A.N.Volkov, D.Ferrari, J.A.Worrall, A.M.Bonvin, and M.Ubbink (2005).
The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK.
  Protein Sci, 14, 799-811.  
16060674 S.Deep, S.C.Im, E.R.Zuiderweg, and L.Waskell (2005).
Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
  Biochemistry, 44, 10654-10668.  
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.  
14736872 J.A.Hoy, S.Kundu, J.T.Trent, S.Ramaswamy, and M.S.Hargrove (2004).
The crystal structure of Synechocystis hemoglobin with a covalent heme linkage.
  J Biol Chem, 279, 16535-16542.
PDB code: 1rtx
15194706 T.A.Clarke, S.C.Im, A.Bidwai, and L.Waskell (2004).
The role of the length and sequence of the linker domain of cytochrome b5 in stimulating cytochrome P450 2B4 catalysis.
  J Biol Chem, 279, 36809-36818.  
12767127 K.H.Lee, and K.Kuczera (2003).
Molecular dynamics simulation studies of cytochrome b5 from outer mitochondrial and microsomal membrane.
  Biopolymers, 69, 260-269.  
14674751 W.Shao, S.C.Im, E.R.Zuiderweg, and L.Waskell (2003).
Mapping the binding interface of the cytochrome b5-cytochrome c complex by nuclear magnetic resonance.
  Biochemistry, 42, 14774-14784.  
11714912 C.Qian, Y.Yao, K.Ye, J.Wang, W.Tang, Y.Wang, W.Wang, J.Lu, Y.Xie, and Z.Huang (2001).
Effects of charged amino-acid mutation on the solution structure of cytochrome b(5) and binding between cytochrome b(5) and cytochrome c.
  Protein Sci, 10, 2451-2459.
PDB code: 1i5u
11246020 D.R.Davydov (2001).
Microsomal monooxygenase in apoptosis: another target for cytochrome c signaling?
  Trends Biochem Sci, 26, 155-160.  
11248680 Y.Wu, Y.Wang, C.Qian, J.Lu, E.Li, W.Wang, J.Lu, Y.Xie, J.Wang, D.Zhu, Z.Huang, and W.Tang (2001).
Solution structure of cytochrome b(5) mutant (E44/48/56A/D60A) and its interaction with cytochrome c.
  Eur J Biochem, 268, 1620-1630.
PDB codes: 1f03 1f04
10852709 F.Arnesano, L.Banci, I.Bertini, D.Koulougliotis, and A.Monti (2000).
Monitoring mobility in the early steps of unfolding: the case of oxidized cytochrome b(5) in the presence of 2 M guanidinium chloride.
  Biochemistry, 39, 7117-7130.  
10842340 J.Wu, J.H.Gan, Z.X.Xia, Y.H.Wang, W.H.Wang, L.L.Xue, Y.Xie, and Z.X.Huang (2000).
Crystal structure of recombinant trypsin-solubilized fragment of cytochrome b(5) and the structural comparison with Val61His mutant.
  Proteins, 40, 249-257.
PDB codes: 1ehb 1es1
10651812 L.Banci, I.Bertini, A.Rosato, and S.Scacchieri (2000).
Solution structure of oxidized microsomal rabbit cytochrome b5. Factors determining the heterogeneous binding of the heme.
  Eur J Biochem, 267, 755-766.
PDB code: 1do9
10095768 F.Arnesano, L.Banci, I.Bertini, I.C.Felli, and D.Koulougliotis (1999).
Solution structure of the B form of oxidized rat microsomal cytochrome b5 and backbone dynamics via 15N rotating-frame NMR-relaxation measurements. Biological implications.
  Eur J Biochem, 260, 347-354.
PDB code: 1bfx
9622481 B.Dangi, S.Sarma, C.Yan, D.L.Banville, and R.D.Guiles (1998).
The origin of differences in the physical properties of the equilibrium forms of cytochrome b5 revealed through high-resolution NMR structures and backbone dynamic analyses.
  Biochemistry, 37, 8289-8302.
PDB codes: 1b5a 1b5b
9748314 J.C.Rodríguez, and M.Rivera (1998).
Conversion of mitochondrial cytochrome b5 into a species capable of performing the efficient coupled oxidation of heme.
  Biochemistry, 37, 13082-13090.  
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
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.

 

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