4LCR | pdb_00004lcr

The crystal structure of di-Zn dihydropyrimidinase in complex with NCBA

• PDB DOI: https://doi.org/10.2210/pdb4LCR/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): Tetraodon nigroviridis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-22 Released: 2013-09-18 
• Deposition Author(s): Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structures of vertebrate dihydropyrimidinase and complexes from Tetraodon nigroviridis with lysine carbamylation: metal and structural requirements for post-translational modification and function.

Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

(2013) J Biological Chem 288: 30645-30658

• PubMed: 24005677 
• DOI: https://doi.org/10.1074/jbc.M113.496778
• Primary Citation Related Structures: 
  4LCQ, 4LCR, 4LCS


• PubMed Abstract: 
  

  Lysine carbamylation, a post-translational modification, facilitates metal coordination for specific enzymatic activities. We have determined structures of the vertebrate dihydropyrimidinase from Tetraodon nigroviridis (TnDhp) in various states: the apoenzyme as well as two forms of the holoenzyme with one and two metals at the catalytic site. The essential active-site structural requirements have been identified for the possible existence of four metal-mediated stages of lysine carbamylation. Only one metal is sufficient for stabilizing lysine carbamylation; however, the post-translational lysine carbamylation facilitates additional metal coordination for the regulation of specific enzymatic activities through controlling the conformations of two dynamic loops, Ala(69)-Arg(74) and Met(158)-Met(165), located in the tunnel for the substrate entrance. The substrate/product tunnel is in the "open form" in the apo-TnDhp, in the "intermediate state" in the monometal TnDhp, and in the "closed form" in the dimetal TnDhp structure, respectively. Structural comparison also suggests that the C-terminal tail plays a role in the enzymatic function through interactions with the Ala(69)-Arg(74) dynamic loop. In addition, the structures of the dimetal TnDhp in complexes with hydantoin, N-carbamyl-β-alanine, and N-carbamyl-β-amino isobutyrate as well as apo-TnDhp in complex with a product analog, N-(2-acetamido)-iminodiacetic acid, have been determined. These structural results illustrate how a protein exploits unique lysines and the metal distribution to accomplish lysine carbamylation as well as subsequent enzymatic functions.

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Organizational Affiliation: 
• From the Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.
the Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan.
the Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan,; the Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 911525.
the Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan,. Electronic address: [e-mail].
From the Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan,; the Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan, and; the Institute of Biotechnology and; University Center for Bioscience and Biotechnology, National Cheng Kung University, 1 University Road, Tainan City 701, Taiwan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 57.19 kDa 
• Atom Count: 3,970 
• Modeled Residue Count: 485 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosome 8 SCAF14545, whole genome shotgun sequence	A	520	Tetraodon nigroviridis	Mutation(s): 0  Gene Names: DPYS, GSTENG00015639001
UniProt
Find proteins for Q4SMR4 (Tetraodon nigroviridis) Explore Q4SMR4  Go to UniProtKB:  Q4SMR4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
URP	B [auth A]	N-(AMINOCARBONYL)-BETA-ALANINE C4 H8 N2 O3 JSJWCHRYRHKBBW-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.204	α = 90
b = 161.204	β = 90
c = 93.803	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Hsieh, Y.C., Chen, M.C., Hsu, C.C., Chan, S.I., Yang, Y.S., Chen, C.J.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary