Structure of PDB 3g1d Chain A

Receptor sequence
>3g1dA (length=218) Species: 187420 (Methanothermobacter thermautotrophicus str. Delta H) [Search protein sequence]
VMDVMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIA
EFRKRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVR
ACLNVAEEMGREVFLLTEMSHPGAEMFIQGAADEIARMGVDLGVKNYVGP
STRPERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYL
ADNPAAAAAGIIESIKDL
3D structure
PDB3g1d Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.
ChainA
Resolution1.5 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 D70 K72 D75
Catalytic site (residue number reindexed from 1) K35 D63 K65 D68
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 U A D20 K42 D70 K72 M126 S127 P180 Q185 G202 R203 D13 K35 D63 K65 M119 S120 P173 Q178 G195 R196 PDBbind-CN: -logKd/Ki=3.48,Ki=330uM
BS02 U A D75 I76 T79 D68 I69 T72 PDBbind-CN: -logKd/Ki=3.48,Ki=330uM
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:3g1d, PDBe:3g1d, PDBj:3g1d
PDBsum3g1d
PubMed19435314
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

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