4OFC

2.0 Angstroms X-ray crystal structure of human 2-amino-3-carboxymuconate-6-semialdehye decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Human alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD): A structural and mechanistic unveiling.

Huo, L.Liu, F.Iwaki, H.Li, T.Hasegawa, Y.Liu, A.

(2015) Proteins 83: 178-187

  • DOI: 10.1002/prot.24722
  • Primary Citation of Related Structures:  4IGN, 4IH3

  • PubMed Abstract: 
  • Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase determines the fate of tryptophan metabolites in the kynurenine pathway by controlling the quinolinate levels for de novo nicotinamide adenine dinucleotide biosynthesis. The unstable nature ...

    Human α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase determines the fate of tryptophan metabolites in the kynurenine pathway by controlling the quinolinate levels for de novo nicotinamide adenine dinucleotide biosynthesis. The unstable nature of its substrate has made gaining insight into its reaction mechanism difficult. Our electron paramagnetic resonance (EPR) spectroscopic study on the Cu-substituted human enzyme suggests that the native substrate does not directly ligate to the metal ion. Substrate binding did not result in a change of either the hyperfine structure or the super-hyperfine structure of the EPR spectrum. We also determined the crystal structure of the human enzyme in its native catalytically active state (at 1.99 Å resolution), a substrate analogue-bound form (2.50 Å resolution), and a selected active site mutant form with one of the putative substrate binding residues altered (2.32 Å resolution). These structures illustrate that each asymmetric unit contains three pairs of dimers. Consistent with the EPR findings, the ligand-bound complex structure shows that the substrate analogue does not directly coordinate to the metal ion but is bound to the active site by two arginine residues through noncovalent interactions.


    Organizational Affiliation

    Department of Chemistry and the Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
A, B, C, D, E, F
335Homo sapiensGene Names: ACMSD
EC: 4.1.1.45
Find proteins for Q8TDX5 (Homo sapiens)
Go to Gene View: ACMSD
Go to UniProtKB:  Q8TDX5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.704α = 90.00
b = 101.082β = 90.00
c = 232.820γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
SERGUIdata collection
DENZOdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2014-12-31
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description