Structure of PDB 3g1v Chain A

Receptor sequence

>3g1vA (length=213) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIAGFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIK

3D structure

• PDB: 3g1v Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
• Chain: A
• Resolution: 1.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K42 G70 K72 D75
• Catalytic site (residue number reindexed from 1): K32 G60 K62 D65
• 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	5FU	A	D20 K42 L123 M126 S127 P180 Q185 G202 R203	D10 K32 L113 M116 S117 P170 Q175 G192 R193	PDBbind-CN: -logKd/Ki=3.19,Ki=645uM BindingDB: Ki=645000nM
BS02	5FU	A	D75 I76 T79	D65 I66 T69	PDBbind-CN: -logKd/Ki=3.19,Ki=645uM BindingDB: Ki=645000nM

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:0044205 'de novo' UMP biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:3g1v, PDBe:3g1v, PDBj:3g1v
• PDBsum: 3g1v
• PubMed: 19435314
• UniProt: O26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)