| Title | Crystal structure of Orotidine 5'-phosphate decarboxylase (TM0332) from Thermotoga maritima at 2.00 A resolution. | | Site | JCSG | | PDB Id | | Target Id | 282207 | | Molecular Characteristics | | Source | Thermotoga maritima | | Alias Ids | TM0332 | Molecular Weight | 22807.49 Da. | | Residues | 201 | Isoelectric Point | 6.97 | | Sequence | mtpvlsldmedpirfidengsfevvkvghnlaihgkkifdelakrnlkiildlkfcdipstversikswd hpaiigftvhscagyesveralsatdkhvfvvvkltsmegsledymdrieklnklgcdfvlpgpwakal rekikgkilvpgirmevkaddqkdvvtleemkgianfavlgreiylsenprekikrikemrl | | | BLAST FFAS |
| Structure Determination | | Method | XRAY | Chains | 1 | | Resolution (Å) | 2.00 | Rfree | 0.22088 | | Matthews' coefficent | 2.58 | Rfactor | 0.18139 | | Waters | 62 | Solvent Content | 52.04 |
| Pathway | | Reactions found in Metabolic Reconstruction: TM0332 | Metabolic Subsystem: Pyrimidine Biosynthesis
Reaction: :
h
Name:H+
Formula:H
KEGG:
C00080
+
orot5p
Name:Orotidine 5'-phosphate
Formula:C10H10N2O11P
KEGG:
C01103
-->
co2
Name:CO2
Formula:CO2
KEGG:
C00011
+
ump
Name:UMP
Formula:C9H11N2O9P
KEGG:
C00105
Name: orotidine-5'-phosphate decarboxylase
Classification: EC:4.1.1.23
|
| Ligand Information | | Ligands | EDO (1,2-ETHANEDIOL) x 9 | | Metals | | | |
Protein Summary
The TM0332 gene of Thermotoga maritima encodes an orotidine 5'-phosphate decarboxylase (OPDase) (PF00215, COG0284, EC 4.1.1.23). The structure adopts a TIM barrel alpha/beta fold and is very similar to other bacterial OPDases including orthologs from Escherichia coli (PDB id: 1l2u, backbone rmsd 1.7 Å over 180 residues, 28% sequence identity), Bacillus subtilis (PDB id: 1dbt, backbone rmsd 1.9 Å over 185 residues, 26% sequence identity) and Geobacillus kaustophilus (PDB id: 2yyu, backbone rmsd 1.8 Å over 182 residues, 26% sequence identity). Further discussion of the structure, active site, catalytic mechanism and conformational changes induced by substrate binding can be found at Harris 2002.
Ligand Summary
References
