Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner
Abstract
:1. Introduction
- With the donation of electrons from the pyruvate, Fld can transport electrons from the phosphoroclastic system to the outer membrane or to the sulfate-reducing system [23]. The other organic source, aldehyde, which is reduced by aldehyde oxidoreductase (AOR), can also produce electrons. The transfer of electrons between AOR and Fld has also been reported [24].
- Through the donation of electrons from molecular dihydrogen, Fld carries the electrons from the outer membrane to the sulfate-reducing system [25]. Although some studies showed that cytochrome c3 and Fld might form a protein complex [26], the exact pathway of the electron transfer between the periplasm and the sulfate-reducing system remains unclear. Among the SRB Desulfovibrio sp., the structures of Flds from Desulfovibrio vulgaris (D. vulgaris) and Desulfovibrio desulfuricans (D. desulfuricans) have been determined [27,28]. The effects of some mutated residues, such as G61V and D95E, interacting with the FMN in three redox states were also studied in D. vulgaris Fld [29,30].
2. Results and Discussion
2.1. Crystal Characterization and X-ray Diffraction
2.2. The Crystal Structure of Fld
2.3. Environment of FMN
2.4. The Dynamic Characteristics in Fld
2.5. The Dimerization and Crystal Packing of Fld
2.6. Comparison with Fld Structures from Desulfovibrio sp
3. Experimental Section
3.1. Protein Purification
3.2. Crystallization
3.3. X-ray Data Collection and Processing
3.4. Structural Determination and Refinement
4. Conclusions
Supplementary Information
ijms-14-01667-s001.pdfAcknowledgments
References
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Data collection | |
---|---|
Wavelength (Å) | 1.00 |
Temperature (K) | 110 |
Space group | P212121 |
Resolution Range (Å) | 30.0–1.21 (1.25–1.21) a |
Cell dimensions (Å) | |
a | 50.20 |
b | 60.37 |
c | 76.25 |
Unique reflections | 71,508 (7049) a |
Completeness (%) | 99.9 (99.7) a |
<I/σ(I)> | 33.9 (3.4) a |
Average redundancy | 7.1 (6.8) a |
Rsymb (%) | 8.7 (71.8%) a |
Mosaicity | 0.28 |
No. of molecules per asymmetric unit | 2 |
Matthews coefficient (Å3 Da−1) | 2.06 |
Solvent content (%) | 40.4 |
Refinement | |
Resolution range (Å) | 30.0–1.3 |
Rworkc/Rfreed (%) | 18.0/21.1 |
No. of atoms | |
Protein | 2152 |
Ligand (FMN) | 61 |
Water molecules | 346 |
B-factors (Å2) | |
Protein | 11.5 |
Ligand (FMN) | 8.0 |
Water molecules | 21.1 |
R.m.s deviations | |
Bond lengths (Å) | 0.027 |
Bond angles (°) | 2.460 |
FMN | Contact | Atoms | Distance (Å) (monomer A) | Distance (Å) (monomer B) |
---|---|---|---|---|
O3P [O] | 12(THR) | N [N] | 2.93 | 2.88 |
14(ASN) | N [N] | 2.93 | 2.92 | |
12(THR) | OG1 [O] | 2.56 | 2.57 | |
O1P [O] | 60(TRP) | NE1[N] | 2.82 | 3.2 |
58(SER) | OG [O] | 2.74 | 2.71 | |
11(THR) | N [N] | 2.82 | 2.78 | |
O2P [O] | 15(THR) | N [N] | 2.73 | 2.71 |
15(THR) | OG1 [O] | 2.75 | 2.76 | |
10(SER) | OG [O] | 2.71 | 2.69 | |
O4′ [O] | 14(ASN) | ND2 [N] | 2.84 | 2.86 |
O2′ [O] | 59(THR) | O [O] | 2.72 | 2.7 |
O2 [O] | 95(ASP) | N [N] | 2.94 | 2.91 |
102(CYS) | N [N] | 2.78 | 2.78 |
Source (chain/residue) | Atoms | Target (chain/residue) | Atoms | Distance (Å) |
---|---|---|---|---|
A/64(GLU) | CB [C] | B/65(ILE) | O [O] | 3.30 |
A/65(ILE) | N [N] | B/65(ILE) | O [O] | 3.20 |
A 65(ILE) | O [O] | B/64(GLU) | CA [C] | 3.35 |
B/65(ILE) | N [N] | 2.82 | ||
A/66(GLU) | CG [C] | B/63(ASP) | O [O] | 3.45 |
A/66(GLU) | CD [C] | B/63(ASP) | O [O] | 3.35 |
A/67(LEU) | N [N] | B/100(TYR) | OH [O] | 3.03 |
A/72(VAL) | CG2 [C] | B/100(TYR) | OH [O] | 3.49 |
A/76(GLU) | OE2 [O] | B/99(THR) | CG2 [C] | 3.44 |
B/99(THR) | OG1 [O] | 2.62 | ||
A/100(TYR) | CD1 [C] | B/75(TYR) | CE2 [C] | 3.49 |
A/106(ASP) | OD1 [O] | B/110(LYS) | CG [C] | 3.16 |
A/109(GLU) | OE1 [O] | B/110(LYS) | CE [C] | 3.33 |
B/110(LYS) | NZ [N] | 2.87 | ||
A/110(LYS) | CB [C] | B/106(ASP) | OD1 [O] | 3.40 |
A/110(LYS) | CD [C] | B/109(GLU) | OE1 [O] | 3.18 |
A/110(LYS) | CE [C] | B/109(GLU) | OE1 [O] | 3.12 |
A/110(LYS) | NZ [N] | B/109(GLU) | CD [C] | 3.45 |
B/109(GLU) | OE1 [O] | 2.74 | ||
B/113(GLU) | CD [C] | 3.25 | ||
B/113(GLU) | OE1 [O] | 2.60 | ||
B/113(GLU) | OE2 [O] | 3.20 | ||
A/114(GLU) | OE2 [O] | B/125(LYS) | NZ [N] | 2.85 |
A/125(LYS) | NZ [N] | B/114(GLU) | OE2 [O] | 2.83 |
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Hsieh, Y.-C.; Chia, T.S.; Fun, H.-K.; Chen, C.-J. Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner. Int. J. Mol. Sci. 2013, 14, 1667-1683. https://doi.org/10.3390/ijms14011667
Hsieh Y-C, Chia TS, Fun H-K, Chen C-J. Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner. International Journal of Molecular Sciences. 2013; 14(1):1667-1683. https://doi.org/10.3390/ijms14011667
Chicago/Turabian StyleHsieh, Yin-Cheng, Tze Shyang Chia, Hoong-Kun Fun, and Chun-Jung Chen. 2013. "Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner" International Journal of Molecular Sciences 14, no. 1: 1667-1683. https://doi.org/10.3390/ijms14011667