Structure of PDB 3p5z Chain B

Receptor sequence

>3p5zB (length=220) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H)

DVMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDII
AEFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSV
RACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVG
PSSRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIY
LADNPAAAAAGIIESIKDLL

3D structure

• PDB: 3p5z Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme.
• Chain: B
• Resolution: 1.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K42 D70 K72 D75
• Catalytic site (residue number reindexed from 1): K36 D64 K66 D69
• 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	D75 I76 T79	D69 I70 T73
BS02	BMP	B	D20 K42 K72 M126 S127 P180 Q185 G202 R203	D14 K36 K66 M120 S121 P174 Q179 G196 R197
BS03	POL	B	A208 N210 A213 A214	A202 N204 A207 A208

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:3p5z, PDBe:3p5z, PDBj:3p5z
• PDBsum: 3p5z
• PubMed: 23030629
• UniProt: O26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)