Structure of PDB 3w07 Chain A

Receptor sequence

>3w07A (length=215) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIESIKDL

3D structure

• PDB: 3w07 Atomic resolution structure of the orotidine 5'-monophosphate decarboxylase product complex combined with surface plasmon resonance analysis: implications for the catalytic mechanism.
• Chain: A
• Resolution: 1.03 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K42 D70 K72 D75
• Catalytic site (residue number reindexed from 1): K32 D60 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	U5P	A	D20 K42 D70 K72 M126 S127 P180 Q185 G202 R203	D10 K32 D60 K62 M116 S117 P170 Q175 G192 R193	MOAD: Kd=0.00042M PDBbind-CN: -logKd/Ki=3.38,Kd=0.42mM

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:3w07, PDBe:3w07, PDBj:3w07
• PDBsum: 3w07
• PubMed: 23395822
• UniProt: O26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)