Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans
Jayson Davidson, Kyndall Nicholas, Jeremy Young, Deborah G. Conrady, Stephen Mayclin, Sandhya Subramanian, Bart L. Staker, Peter J. Myler and Oluwatoyin A. Asojo [1]
Molecular Tour
The high-resolution structure of a putative short-chain reductase from the commercially important bacteria Paraburkholderia xenovorans is reported (PxSDR). The reported apo structure of PxSDR was determined in the monoclinic space group P21 as a . P. xenovorans degrades organic wastes like polychlorinated biphenyls. PxSDR shares less than 37% sequence identity with any known structure (see static image below) and assembles as a prototypical SDR tetramer.
![Structural and primary-sequence alignment of PxSDR with the closest structures identified by PDBeFold. Also shown is the percent identity matrix generated with Clustal2.1. The structures are PDB entry 5jc8 (the apo structure of PxSDR), PDB entry 1iy8 (the crystal structure of levodione reductase from Leifsonia aquatica), PDB entry 3ftp [3-ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei], PDB entry 6t6n [Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH] and PDB entry 6ixm (ketone reductase ChKRED20 from the genome of Chryseobacterium). The secondary-structure elements shown are α-helices (α), 310-helices (η), β-strands (β) and β-turns (TT). Identical residues are shown in white on a red background and conserved residues are shown in red. This figure was generated using ESPript (Gouet et al., 1999, 2003),.](/wiki/images/thumb/7/7a/Figure2t1.png/450px-Figure2t1.png)
Structural and primary-sequence alignment of
PxSDR with the closest structures identified by
PDBeFold. Also shown is the percent identity matrix generated with
Clustal2.1. The structures are PDB entry
5jc8 (the apo structure of
PxSDR), PDB entry
1iy8 (the crystal structure of levodione reductase from
Leifsonia aquatica), PDB entry
3ftp [3-ketoacyl-(acyl-carrier-protein) reductase from
Burkholderia pseudomallei], PDB entry
6t6n [
Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH] and PDB entry
6ixm (ketone reductase ChKRED20 from the genome of
Chryseobacterium). The secondary-structure elements shown are α-helices (α), 3
10-helices (η), β-strands (β) and β-turns (TT). Identical residues are shown in white on a red background and conserved residues are shown in red. This figure was generated using
ESPript (Gouet et al., 1999, 2003)
[2],
[3].
As expected, there is some conformational flexibility and differences between the , which explains substrate specificity. The substrate-binding cavity is labeled in royalblue. The superposed structures are PDB entry 5jc8 (apo structure of PxSDR, whitesmoke), PDB entry 1iy8 (crystal structure of levodione reductase from Leifsonia aquatica, red), PDB entry 3ftp [3-ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei, yellow], PDB entry 6t6n [Klebsiella pneumoniae
FabG2(NADH-dependent) in complex with NADH, wheat] and PDB entry 6ixm (ketone reductase ChKRED20 from the genome of Chryseobacterium, aquamarine). The cofactor, NADH (magenta) and substrate, (4R)-2-methylpentane-2,4-diol (royalblue), are from PDB entry 1iy8. Structures were superposed with PyMOL. Uniquely, the of PxSDR is not well conserved and differs from other SDRs. The cofactor-binding cavity is labeled in magenta. PxSDR has an additional seven-amino acids that form an within the co-factor binding cavity. Further studies are required to determine how these differences affect the enzymatic functions of the SDR. This project is an educational collaboration between the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and Hampton University where undergraduate students are engaged in structure-function analysis and publication of structures solved by the SSGCID.
PDB reference: putative short-chain reductase, 5jc8.
References
- ↑ Davidson J, Nicholas K, Young J, Conrady DG, Mayclin S, Subramanian S, Staker BL, Myler PJ, Asojo OA. Crystal structure of a putative short-chain dehydrogenase/reductase from Paraburkholderia xenovorans. Acta Crystallogr F Struct Biol Commun. 2022 Jan 1;78(Pt 1):25-30. doi:, 10.1107/S2053230X21012632. Epub 2022 Jan 1. PMID:34981772 doi:http://dx.doi.org/10.1107/S2053230X21012632
- ↑ Gouet P, Courcelle E, Stuart DI, Metoz F. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 1999 Apr;15(4):305-8. doi: 10.1093/bioinformatics/15.4.305. PMID:10320398 doi:http://dx.doi.org/10.1093/bioinformatics/15.4.305
- ↑ Gouet P, Robert X, Courcelle E. ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 2003 Jul 1;31(13):3320-3. PMID:12824317
![Structural and primary-sequence alignment of PxSDR with the closest structures identified by PDBeFold. Also shown is the percent identity matrix generated with Clustal2.1. The structures are PDB entry 5jc8 (the apo structure of PxSDR), PDB entry 1iy8 (the crystal structure of levodione reductase from Leifsonia aquatica), PDB entry 3ftp [3-ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei], PDB entry 6t6n [Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH] and PDB entry 6ixm (ketone reductase ChKRED20 from the genome of Chryseobacterium). The secondary-structure elements shown are α-helices (α), 310-helices (η), β-strands (β) and β-turns (TT). Identical residues are shown in white on a red background and conserved residues are shown in red. This figure was generated using ESPript (Gouet et al., 1999, 2003),.](/wiki/index.php/Image:Figure2t1.png)
