DHRS1 Results
Results/structure Dehydrogenase/reductase SDR family member 1 has highly conserved structure compared across the SDR family.
SDR family is part of the Super Family; NAD(P)-binding Rossmann-fold domain proteins all of which have the Rossmann-fold domain, which is characterised a central β-sheet surrounded by α-helicies. This buts them in the Alpha and Beta proteins (α/β) class.
Some key residues are conserved across the entire family. Notable a Tyrosine that binds NADPH. It is part of a larger motif (SxxxxxxxxxxxxYxxxK) that includes two other residues involved in binding NADPH.
There is another highly conserved motif (LDVLD) involved in the initial folding of the protein and forms part of the hydrophobic core.
BLAST
The protein sequence for the SDR family member 1 protein being investigated was downloaded from the PDB site, using the accession code 2qq5. This was then iteratively searched in blastp using an offline, non redundant copy of the database produced on the 28th of April 2008.
MULTIPLE SEQUENCE ALIGNMENT
The results from the blast search were then screened and a selection was of these results were used for a multiple sequence alignment using ClustalX. This result was boostrapped and these values checked and more sequences were added to improve the resolution of specific branches. A bootstrapped phylogram was produces, aswell as a radial tree.
Table 1
PDB/chain identifiers and structural alignment statistics for DALI search
No: Chain Z rmsd lali nres %id Description 1: 2qq5-A 48.1 0.0 238 238 100 MOL:DEHYDROGENASE/REDUCTASE SDR1; 2: 2uvd-A 29.6 2.1 220 246 27 MOL: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE; 3: 1yde-F 29.3 2.1 216 256 29 MOL: RETINAL DEHYDROGENASE/REDUCTASE 3; 4: 1vl8-B 29.1 2.0 220 252 27 MOL: GLUCONATE 5-DEHYDROGENASE; 5: 2bgk-A 29.0 2.1 219 267 25 MOL: RHIZOME SECOISOLARICIRESINOL DEHYDROGENASE; 6: 2q2q-D 28.9 2.0 217 255 26 MOL: BETA-D-HYDROXYBUTYRATEDEHYDROGENASE; 7: 1rwb-F 28.8 2.2 221 261 24 MOL: GLUCOSE 1-DEHYDROGENASE; 8: 1rwb-A 28.8 2.3 222 261 24 MOL: GLUCOSE 1-DEHYDROGENASE; 9: 1gee-A 28.8 2.3 222 261 24 MOL: GLUCOSE 1-DEHYDROGENASE; 10: 1gco-A 28.8 2.3 222 261 24 MOL: GLUCOSE DEHYDROGENASE; 11: 2zat-A 28.7 2.1 221 251 23 MOL: DEHYDROGENASE/REDUCTASE SDR4; 12: 1gee-B 28.7 2.3 221 261 24 MOL: GLUCOSE 1-DEHYDROGENASE; 13: 1gco-E 28.7 2.3 221 261 24 MOL: GLUCOSE DEHYDROGENASE;