Structure of PDB 1km1 Chain B

Receptor sequence
>1km1B (length=211) Species: 145262 (Methanothermobacter thermautotrophicus) [Search protein sequence]
VMNRLILAMDLMNRDDALRVTGEVREYIDTVKIGYPLVLSEGMDIIAEFR
KRFGCRIIADFKVADIPETNEKICRATFKAGADAIIVHGFPGADSVRACL
NVAEEMGREVFLLTEMAHPGAEMFIQGAADEIARMGVDLGVKNYVGPSTR
PERLSRLREIIGQDSFLISPGVGAQGGDPGETLRFADAIIVGRSIYLADN
PAAAAAGIIES
3D structure
PDB1km1 Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.
ChainB
Resolution1.6 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 UP6 B D75 I76 T79 D65 I66 T69 BindingDB: Ki=12400nM
BS02 UP6 B D20 K42 K72 M126 P180 Q185 G202 R203 D10 K32 K62 M116 P170 Q175 G192 R193 BindingDB: Ki=12400nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1km1, PDBe:1km1, PDBj:1km1
PDBsum1km1
PubMed11900543
UniProtO26232|PYRF_METTH Orotidine 5'-phosphate decarboxylase (Gene Name=pyrF)

[Back to BioLiP]