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Pochapsky, T. C., Jain, N. U., Kuti, M., Lyons, T. A., and Heymont, J., "A Refined Model for the Solution Structure of Oxidized Putidaredoxin", Biochemistry, 38, 4681-4690 (1999).
A refined model for the solution structure of oxidized putidaredoxin.

Sequential 1H resonance assignments and secondary structural features of putidaredoxin (Pdx), a 106-residue globular protein consisting of a single polypeptide chain and a [2Fe-2S] cluster, are reported. No crystal structure has been obtained for Pdx or for any closely homologous protein. The sequentially assigned resonances represent ca. 83% of all the protons in Pdx and a large majority of those protons which are unaffected by the paramagnetism of the iron-sulfur cluster. A total of three alpha-helices, two beta-sheets, and two type I beta-turns have been identified from NOE (nuclear Overhauser effect) patterns. Besides the extensive beta-sheet described previously, a second sheet is identified, consisting of two short antiparallel strands (Ile 89-Thr 91 and Val 21-Leu 23), one of which ends in a tight type I turn (Thr 91-Pro 92-Glu 93-Leu 94). One short helix (Ala 26-Gly 31) and a second longer helical region (Glu 54-Cys 73) are present. This second helical region is discontinuous, breaking at Pro 61, resuming at Glu 65, and ending at Cys 73. The functionally important C-terminal tryptophan residue has been identified, and some structural constraints on this residue are described. Previously reported functional data concerning Pdx are discussed in light of present structural information. Finally, approaches to the determination of a high-resolution solution structure of the protein are discussed.
Ye, X. M., Pochapsky, T. C. and Pochapsky, S. S., "1H NMR Sequential Assignments and Identification of Secondary Structural Elements in Oxidized Putidaredoxin, an Electron-transfer Protein from Pseudomonas," Biochemistry 31, 1961-1968 (1992)
1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas.

Multidimensional NMR methods were used to obtain 1H-15N correlations and 15N resonance assignments for amide and side-chain nitrogens of oxidized and reduced putidaredoxin (Pdx), the Fe2S2 ferredoxin, which acts as the physiological reductant of cytochrome P-450cam (CYP101). A model for the solution structure of oxidized Pdx has been determined recently using NMR methods (Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA, 1994, Biochemistry 33:6424-6432) and redox-dependent 1H NMR spectral features have been described (Pochapsky TC, Ratnaswamy G, Patera A, 1994, Biochemistry 33:6433-6441). 15N assignments were made with NOESY-(1H/15N) HMQC and TOCSY-(1H/15N) HSQC spectra obtained using samples of Pdx uniformly labeled with 15N. Local dynamics in both oxidation states of Pdx were then characterized by comparison of residue-specific amide proton exchange rates, which were measured by a combination of saturation transfer and H2O/D2O exchange methods at pH 6.4 and 7.4 (uncorrected for isotope effects). In general, where exchange rates for a given site exhibit significant oxidation-state dependence, the oxidized protein exchanges more rapidly than the reduced protein. The largest dependence of exchange rate upon oxidation state is found for residues near the metal center and in a region of compact structure that includes the loop-turn Val 74-Ser 82 and the C-terminal residues (Pro 102-Trp 106). The significance of these findings is discussed in light of the considerable dependence of the binding interaction between Pdx and CYP101 upon the oxidation state of Pdx.
Lyons, T. A., Ratnaswamy, G. and Pochapsky, T. C., "Redox-dependent Dynamics of Putidaredoxin Characterized by Amide Proton Exchange," Protein Sci. 5, 627-639 (1996).
Protein science : a publication of the Protein Society
Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange.

A considerable degree of variability exists in the way that 1H, 13C and 15N chemical shifts are reported and referenced for biomolecules. In this article we explore some of the reasons for this situation and propose guidelines for future chemical shift referencing and for conversion from many common 1H, 13C and 15N chemical shift standards, now used in biomolecular NMR, to those proposed here.

Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J.,
Oldfield, E., Markley, J. L., and Sykes, B. D.
J. Biomol. NMR 6, 135-140 (1995).

1H, 13C and 15N chemical shift referencing in biomolecular NMR.

"Recommendations for Presentations of NMR Structures of Proteins and Nucleic Acids," IUPAC/IUB Draft version.

Crystal Structure Of C73sC85S MUTANT OF PUTIDAREDOXIN, A [2FE-2s] Ferredoxin From Pseudomonas Putida, At 1.47a Resolution

Crystal Structure Of C73s Mutant Of Putidaredoxin, A [2fe- 2s] Ferredoxin From Pseudomonas Putida, At 1.65a Resolution

An Nmr-Derived Model For The Solution Structure Of Oxidized Putidaredoxin, A 2fe, 2-S Ferredoxin From Pseudomonas

Putidaredoxin (Fe2s2 Ferredoxin), C73g Mutant

Crystal Structure Of Oxidized C73sC85S PUTIDAREDOXIN, A [2fe-2s] Ferredoxin From Pseudomonas Putida

Structure Of Reduced C73s/c85s Putidaredoxin, A [2fe-2s] Ferredoxin From Pseudomonas Putida

Structure Of Oxidized C73s Putidaredoxin From Pseudomonas Putida

Crystal Structure Of Reduced C73s Putidaredoxin From Pseudomonas Putida

Rdc-Refined Solution Nmr Structure Of Reduced Putidaredoxin

Rdc-Refined Solution Nmr Structure Of Oxidized Putidaredoxin

The Structure Of The Complex Of Cytochrome P450cam And Its Electron Donor Putidaredoxin Determined By Paramagnetic Nmr Spectros

Crystal Structure Of The Covalent Putidaredoxin Reductase- Putidaredoxin Complex

Crystal Structure Of The Electron Transfer Complex Of Cytochrome P450cam With Putidaredoxin

Crystal Structure Of Cytochrome P450cam-putidaredoxin Complex

Crystal Structure Of Reduced Cytochrome P450cam-putidaredoxin Complex Bound To Camphor And 5-exo-hydroxycamphor

13C and Stereospecific 13C and 1H Resonance Assignments for Oxidized Putidaredoxin