4IEP

unliganded Cysteine Dioxygenase at pH 4.5 in the presence of Cys

Summary for 4IEP

• Entry DOI: 10.2210/pdb4iep/pdb
• Related: 4IEO 4IEQ 4IER 4IES 4IET 4IEU 4IEV 4IEW 4IEX 4IEY 4IEZ 4IF0 4IF1
• Descriptor: Cysteine dioxygenase type 1, FE (II) ION (3 entities in total)
• Functional Keywords: cupin fold, catalyzes oxidation, cysteine to cysteine sulfinate, c93-y157 crosslink, cytosol, oxidoreductase
• Biological source: Rattus norvegicus (brown rat,rat,rats)
• Total number of polymer chains: 1
• Total formula weight: 23114.73

Authors

Driggers, C.M.,Cooley, R.B.,Karplus, P.A. (deposition date: 2012-12-13, release date: 2013-06-26, Last modification date: 2024-10-09)

Primary citation

Driggers, C.M.,Cooley, R.B.,Sankaran, B.,Hirschberger, L.L.,Stipanuk, M.H.,Karplus, P.A.
Cysteine Dioxygenase Structures from pH4 to 9: Consistent Cys-Persulfenate Formation at Intermediate pH and a Cys-Bound Enzyme at Higher pH.
J.Mol.Biol., 425:3121-3136, 2013

PubMed Abstract: Mammalian cysteine dioxygenase (CDO) is a mononuclear non-heme iron protein that catalyzes the conversion of cysteine (Cys) to cysteine sulfinic acid by an unclarified mechanism. One structural study revealed that a Cys-persulfenate (or Cys-persulfenic acid) formed in the active site, but quantum mechanical calculations have been used to support arguments that it is not an energetically feasible reaction intermediate. Here, we report a series of high-resolution structures of CDO soaked with Cys at pH values from 4 to 9. Cys binding is minimal at pH≤5 and persulfenate formation is consistently seen at pH values between 5.5 and 7. Also, a structure determined using laboratory-based X-ray diffraction shows that the persulfenate, with an apparent average O-O separation distance of ~1.8Å, is not an artifact of synchrotron radiation. At pH≥8, the active-site iron shifts from 4- to 5-coordinate, and Cys soaks reveal a complex with Cys, but no dioxygen, bound. This 'Cys-only' complex differs in detail from a previously published 'Cys-only' complex, which we reevaluate and conclude is not reliable. The high-resolution structures presented here do not resolve the CDO mechanism but do imply that an iron-bound persulfenate (or persulfenic acid) is energetically accessible in the CDO active site, and that CDO active-site chemistry in the crystals is influenced by protonation/deprotonation events with effective pKa values near ~5.5 and ~7.5 that influence Cys binding and oxygen binding/reactivity, respectively. Furthermore, this work provides reliable ligand-bound models for guiding future mechanistic considerations.

PubMed: 23747973
DOI: 10.1016/j.jmb.2013.05.028

Experimental method

X-RAY DIFFRACTION (1.45 Å)