› 7asq

X-ray diffraction
0.95Å resolution

Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the reaction product UMP at 0.95 Angstrom resolution

Released:
DOI: 10.2210/pdb7asq/pdb
PDB entry 7asq coloured by chain, front view.
PDB entry 7asq coloured by chain, side view.
PDB entry 7asq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis
Rindfleisch S, Krull M, Uranga J, Schmidt T, Rabe von Pappenheim F, Kirck LL, Balouri A, Schneider T, Chari A, Kluger R, Bourenkov G, Diederichsen U, Mata RA, Tittmann K
Nat Catal 5 332-341 (2022)

Function and Biology Details

Reactions catalysed: 
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
Orotidine 5'-phosphate = UMP + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145693 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine 5'-monophosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 258 amino acids
Theoretical weight: 28.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11172 (Residues: 224-480; Coverage: 54%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family

Ligands and Environments

4 bound ligands:
Ligand GOL 1 x GOL
Ligand U5P 1 x U5P
Ligand SO4 2 x SO4
Ligand NA 1 x NA
1 modified residue:
Ligand CSS 1 x CSS

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
Spacegroup: C2221
Unit cell:
a: 77.67Å b: 116.86Å c: 61.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.108 0.107 0.12
Expression system: Escherichia coli BL21(DE3)

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