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PDBsum entry 1axx
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Electron transport PDB id
1axx

 

 

 

 

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Contents
Protein chain
94 a.a. *
Ligands
HEM
* Residue conservation analysis
PDB id:
1axx
Name: Electron transport
Title: The solution structure of oxidized rat microsomal cytochrome b5, nmr, 19 structures
Structure: Cytochrome b5. Chain: a. Fragment: soluble domain. Engineered: yes. Other_details: from rat microsomal membrane
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver. Organelle: microsome. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 19 models
Authors: F.Arnesano,L.Banci,I.Bertini,I.C.Felli
Key ref:
F.Arnesano et al. (1998). The solution structure of oxidized rat microsomal cytochrome b5. Biochemistry, 37, 173-184. PubMed id: 9425037 DOI: 10.1021/bi971896w
Date:
22-Oct-97     Release date:   04-Mar-98    
PROCHECK
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 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1021/bi971896w Biochemistry 37:173-184 (1998)
PubMed id: 9425037  
 
 
The solution structure of oxidized rat microsomal cytochrome b5.
F.Arnesano, L.Banci, I.Bertini, I.C.Felli.
 
  ABSTRACT  
 
The solution structure of oxidized rat microsomal cytochrome b5 has been obtained from 1H NMR spectra measured at 800 MHz. The available assignment has been extended to 78% of the total protons and 95% of the residues. From 1372 meaningful NOEs, a family of 40 structures has been obtained through the program DYANA; 235 pseudocontact shifts have been then added as further constraints, obtaining an essentially similar family of structures. This latter family has been further refined through restrained energy minimization. The final RMSD values with respect to the average structure are 0.58 +/- 0.10 A and 1.05 +/- 0.11 A for backbone and heavy atoms, respectively. The high quality of the structure allows meaningful comparisons with the solution structure of the reduced protein, with the X-ray and solution structures of the oxidized bovine isoenzyme, and with the solution structure of the apoprotein. Upon loss of one electron, the heme plane undergoes a change in its orientation, possibly due to the change of the total charge. Propionate 7 appears to have a conformation which is dependent on the oxidation state of the iron. Helices alpha2 and alpha4 also experience changes in their average positions in the two oxidation states. Finally, the backbone NHs experience different exchange properties in the two oxidation states. While those present in the beta sheets forming the basis of the heme pocket are nonexchanging in both oxidation states, the NHs in the helices forming the heme-binding pocket are exchanging with the bulk solvent in the oxidized form, indicating larger local mobility in this state. This observation could suggest that, to optimize the electron transfer process, the local mobility should be properly tuned.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18398853 R.B.Davis, and J.T.Lecomte (2008).
Structural propensities in the heme binding region of apocytochrome b5. I. Free peptides.
  Biopolymers, 90, 544-555.  
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.  
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
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.  
17002396 V.Bondarenko, S.Dewilde, L.Moens, and G.N.La Mar (2006).
Solution 1H NMR characterization of the axial bonding of the two His in oxidized human cytoglobin.
  J Am Chem Soc, 128, 12988-12999.  
16342963 K.Ghosh, A.M.Thompson, R.A.Goldbeck, X.Shi, S.Whitman, E.Oh, Z.Zhiwu, C.Vulpe, and T.R.Holman (2005).
Spectroscopic and biochemical characterization of heme binding to yeast Dap1p and mouse PGRMC1p.
  Biochemistry, 44, 16729-16736.  
15240483 A.Giachetti, G.L.La Penna, A.Perico, and L.Banci (2004).
Modeling the backbone dynamics of reduced and oxidized solvated rat microsomal cytochrome b5.
  Biophys J, 87, 498-512.  
15020591 H.M.Girvan, K.R.Marshall, R.J.Lawson, D.Leys, M.G.Joyce, J.Clarkson, W.E.Smith, M.R.Cheesman, and A.W.Munro (2004).
Flavocytochrome P450 BM3 mutant A264E undergoes substrate-dependent formation of a novel heme iron ligand set.
  J Biol Chem, 279, 23274-23286.  
15273310 Q.Zhang, C.Cao, Z.Q.Wang, Y.H.Wang, H.Wu, and Z.X.Huang (2004).
The comparative study on the solution structures of the oxidized bovine microsomal cytochrome b5 and mutant V45H.
  Protein Sci, 13, 2161-2169.
PDB codes: 1nx7 1sh4
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.  
12770897 M.Assfalg, I.Bertini, P.Turano, A.Grant Mauk, J.R.Winkler, and H.B.Gray (2003).
15N-1H Residual dipolar coupling analysis of native and alkaline-K79A Saccharomyces cerevisiae cytochrome c.
  Biophys J, 84, 3917-3923.  
12237467 B.J.Goodfellow, S.G.Nunes, F.Rusnak, I.Moura, C.Ascenso, J.J.Moura, B.F.Volkman, and J.L.Markley (2002).
Zinc-substituted Desulfovibrio gigas desulforedoxins: resolving subunit degeneracy with nonsymmetric pseudocontact shifts.
  Protein Sci, 11, 2464-2470.  
11988476 M.Ubbink, J.A.Worrall, G.W.Canters, E.J.Groenen, and M.Huber (2002).
Paramagnetic resonance of biological metal centers.
  Annu Rev Biophys Biomol Struct, 31, 393-422.  
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
11509552 I.Bertini, D.A.Bryant, S.Ciurli, A.Dikiy, C.O.Fernández, C.Luchinat, N.Safarov, A.J.Vila, and J.Zhao (2001).
Backbone dynamics of plastocyanin in both oxidation states. Solution structure of the reduced form and comparison with the oxidized state.
  J Biol Chem, 276, 47217-47226.
PDB codes: 1jxd 1jxf
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.  
10684632 F.Arnesano, L.Banci, I.Bertini, S.Ciofi-Baffoni, T.L.Woodyear, C.M.Johnson, and P.D.Barker (2000).
Structural consequences of b- to c-type heme conversion in oxidized Escherichia coli cytochrome b562.
  Biochemistry, 39, 1499-1514.
PDB code: 1qq3
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
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.  
10213609 E.M.Storch, J.S.Grinstead, A.P.Campbell, V.Daggett, and W.M.Atkins (1999).
Engineering out motion: a surface disulfide bond alters the mobility of tryptophan 22 in cytochrome b5 as probed by time-resolved fluorescence and 1H NMR experiments.
  Biochemistry, 38, 5065-5075.  
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.  
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
10393541 F.Arnesano, L.Banci, I.Bertini, J.Faraone-Mennella, A.Rosato, P.D.Barker, and A.R.Fersht (1999).
The solution structure of oxidized Escherichia coli cytochrome b562.
  Biochemistry, 38, 8657-8670.
PDB code: 1qpu
10226044 I.Bertini, and C.Luchinat (1999).
New applications of paramagnetic NMR in chemical biology.
  Curr Opin Chem Biol, 3, 145-151.  
10572010 S.Manyusa, G.Mortuza, and D.Whitford (1999).
Analysis of folding and unfolding reactions of cytochrome b5.
  Biochemistry, 38, 14352-14362.  
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
9818268 D.A.Case (1998).
The use of chemical shifts and their anisotropies in biomolecular structure determination.
  Curr Opin Struct Biol, 8, 624-630.  
9836603 F.Arnesano, L.Banci, I.Bertini, and D.Koulougliotis (1998).
Solution structure of oxidized rat microsomal cytochrome b5 in the presence of 2 M guanidinium chloride: monitoring the early steps in protein unfolding.
  Biochemistry, 37, 17082-17092.
PDB code: 1blv
9724546 L.Banci, I.Bertini, C.Cavazza, I.C.Felli, and D.Koulougliotis (1998).
Probing the backbone dynamics of oxidized and reduced rat microsomal cytochrome b5 via 15N rotating frame NMR relaxation measurements: biological implications.
  Biochemistry, 37, 12320-12330.  
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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