Structure of PDB 3nqd Chain B

Receptor sequence
>3nqdB (length=218) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence]
MDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAE
FRKRFGCRIIADFKVADIPETNEKICRATFKAGADAITVHGFPGADSVRA
CLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGPS
TRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLA
DNPAAAAAGIIESIKDLL
3D structure
PDB3nqd Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site.
ChainB
Resolution1.423 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K42 Y45 P46 D70 K72 D75 I76 I83
Catalytic site (residue number reindexed from 1) K34 Y37 P38 D62 K64 D67 I68 I75
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 D67 I68 T71
BS02 BMP B D20 K42 K72 M126 S127 P180 Q185 G202 R203 D12 K34 K64 M118 S119 P172 Q177 G194 R195
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

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Cellular Component
External links
PDB RCSB:3nqd, PDBe:3nqd, PDBj:3nqd
PDBsum3nqd
PubMed21870810
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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