7Q1H

Variant D312N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the substrate OMP at 1.31 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb7Q1H/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-20 Released: 2022-05-04 
• Deposition Author(s): Rabe von Pappenheim, F., Kirck, L.L.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.178 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Literature

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, L.L., Balouri, A., Schneider, T., Chari, A., Kluger, R., Bourenkov, G., Diederichsen, U., Mata, R.A., Tittmann, K.

(2022) Nat Catal 5: 332-341

• DOI: https://doi.org/10.1038/s41929-022-00771-w

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.78 kDa 
• Atom Count: 2,666 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uridine 5'-monophosphate synthase	A	258	Homo sapiens	Mutation(s): 1  Gene Names: UMPS, OK/SW-cl.21 EC: 2.4.2.10 (PDB Primary Data), 4.1.1.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens) Explore P11172  Go to UniProtKB:  P11172
PHAROS:  P11172 GTEx:  ENSG00000114491

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OMP (Subject of Investigation/LOI)	B [auth A]	OROTIDINE-5'-MONOPHOSPHATE C10 H13 N2 O11 P KYOBSHFOBAOFBF-XVFCMESISA-N
PRO	D [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.31 Å
• R-Value Free: 0.178 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.36	α = 90
b = 116.318	β = 90
c = 62.091	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Rabe von Pappenheim, F., Kirck, L.L.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description