Structure of PDB 1dqx Chain B

Receptor sequence

>1dqxB (length=267) Species: 4932 (Saccharomyces cerevisiae)

MHKATYKERAATHPSPVAAKLFNIMHEKQTNLCASLDVRTTKELLELVEA
LGPKICLLKTHVDILTDFSMEGTVKPLKALSAKYNFLLFEDRKFADIGNT
VKLQYSAGVYRIAEWADITNAHGVVGPGIVSGLKQAAEEVTKEPRGLLML
AELSCKGSLSTGEYTKGTVDIAKSDKDFVIGFIAQRDMGGRDEGYDWLIM
TPGVGLDDKGDALGQQYRTVDDVVSTGSDIIIVGRGLFAKGRDAKVEGER
YRKAGWEAYLRRCGQQD

3D structure

• PDB: 1dqx Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.
• Chain: B
• Resolution: 2.4 Å

Enzymatic activity

• Enzyme Commision number: 4.1.1.23: orotidine-5'-phosphate decarboxylase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	BMP	B	D96 I97 T100	D96 I97 T100	MOAD: Ki=9pM PDBbind-CN: -logKd/Ki=11.05,Ki=9pM BindingDB: Ki=0.0090nM
BS02	BMP	B	S35 D37 K59 H61 D91 K93 L153 S154 P202 Q215 Y217 G234 R235	S35 D37 K59 H61 D91 K93 L153 S154 P202 Q215 Y217 G234 R235	MOAD: Ki=9pM PDBbind-CN: -logKd/Ki=11.05,Ki=9pM BindingDB: Ki=0.0090nM

Gene Ontology

Molecular Function

• GO:0004590 orotidine-5'-phosphate decarboxylase activity
• GO:0016831 carboxy-lyase activity

Biological Process

• GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
• GO:0006221 pyrimidine nucleotide biosynthetic process
• GO:0006222 UMP biosynthetic process
• GO:0044205 'de novo' UMP biosynthetic process
• GO:0055086 nucleobase-containing small molecule metabolic process
• GO:0072528 pyrimidine-containing compound biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:1dqx, PDBe:1dqx, PDBj:1dqx
• PDBsum: 1dqx
• PubMed: 10681417
• UniProt: P03962|PYRF_YEAST Orotidine 5'-phosphate decarboxylase (Gene Name=URA3)