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. Author manuscript; available in PMC: 2020 May 7.
Published in final edited form as: Structure. 2019 Mar 21;27(5):794–805.e4. doi: 10.1016/j.str.2019.03.002

Table 2.

Comparison of Human SQOR with Bacterial H2S-Oxidizing Enzymes

Structural Comparison
Electrostatics
Distance (Å)
Active-Site Accessibility
Protein (pdb code) RMSD (Å) No. of Cα Matches FAD Attachment Net Charge (pl)a Membrane- vs Solvent-Facing Surfacesb CysP:SG to CysD:SGc FAD:C4a to
Loop Above re-face of FADd re-face of FAD Active-Site Cysteines
CysP:SG CysD:SG
Human SQOR (PDB: 6MO6) noncovalent positive (9.02) polarized 3.4 3.5 P195-G203 obstructed CysD: close to the surface, accessible via a short channel; CysP: shielded

A. vinosum FCSD (PDB: 1fcd) 2.60 245 covalente negative (5.28) NA 2.1 3.3 P154-P162 obstructed on the surface, solvent exposed

T. tepidum FCSD (PDB: 3vrd) 2.61 241 covalente negative (5.55) NA 4.9 3.5 P154-P162 obstructed on the surface, solvent exposed

T. paradoxus FCSD (PDB: 5n1t) 2.58 239 covalente negative (5.53) NA 4.7 3.5 P186-P194 obstructed on the surface, solvent exposed

A. aeolicus SQOR (PDB: 3hyw) 2.25 212 covalente negative (6.53) polarized 8.1, 8.3, 9.0, 9.3f 6.1, 6.2f 5.7, 6.9f I151-C156 accessible cavity, accommodates sulfur polymerization products accessible via channels

A. ferrooxidans SQOR (PDB: 3t31) 2.91 248 noncovalent negative (6.48) polarized 6.7, 6.8g 6.0 4.7, 5.2g M155-C160 partially shielded, but solvent accessible accessible via channels

A. ambivalens SQOR (PDB: 3h8l) 2.11 221 covalente negative (6.33) ND 6.5, 7.1g 4.9 7.4, 7.6g G154-E179 partially shielded, but solvent accessible accessible via a channel
a

Net charge at pH 7.4 estimated based on the calculated isoelectric point (pI).

b

Solvent refers to the inner mitochondrial matrix (human SQOR) or the periplasmic space (bacterial SQORs), respectively. The property is not applicable (NA) for FCSDs, which are soluble proteins. Electrostatic surface properties were not determined (ND) for A. ambivalens SQOR because no interpretable electron density was observed for the C-terminal membrane-binding domain.

c

The proximal active-site cysteine (CysP) is closer to the N terminus of the protein than the distal cysteine (CysD). CysP:SG is also closer to FAD:C4a in human SQOR, FCSD and some bacterial SQORs. (CysP) = Cys201 (human); Cys161 (A. vinosum FCSD); Cys161 (T. tepidum FCSD); Cys193 (T. paradoxus FCSD); Cys156 (A. aeolicus SQOR); Cys160 (A. ferrooxidans SQOR); Cys178 (A. ambivalens SQOR). CysD = Cys379 (human); Cys337 (A. vinosum FCSD); Cys337 (T. tepidum FCSD); Cys364 (T. paradoxus FCSD); Cys347 (A. aeolicus SQOR); Cys356 (A. ferrooxidans SQOR); Cys350 (A. ambivalens SQOR).

d

The loop from the second Rossmann fold in human SQOR, FCSDs and bacterial SQOR’s includes CysP.

e

Thioether link between FAD:C8M and a cysteine residue: Cys42, A. vinosum FCSD; Cys42, T. tepidum FCSD; Cys73, T. paradoxus FCSD; Cys124, A. aeolicus SQOR; Cys129, A. ambivalens SQOR.

f

Two alternate conformations are observed for both CysP and CysD.

g

Two alternate conformations are observed for CysD.