4LHP

Crystal Structure of Native FG41Malonate Semialdehyde Decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Kinetic, Mutational, and Structural Analysis of Malonate Semialdehyde Decarboxylase from Coryneform Bacterium Strain FG41: Mechanistic Implications for the Decarboxylase and Hydratase Activities.

Guo, Y.Serrano, H.Poelarends, G.J.Johnson, W.H.Hackert, M.L.Whitman, C.P.

(2013) Biochemistry 52: 4830-4841

  • DOI: https://doi.org/10.1021/bi400567a
  • Primary Citation of Related Structures:  
    3MJZ, 3MLC, 4LHO, 4LHP

  • PubMed Abstract: 

    Malonate semialdehyde decarboxylase from Pseudomonas pavonaceae 170 (designated Pp MSAD) is in a bacterial catabolic pathway for the nematicide 1,3-dichloropropene. MSAD has two known activities: it catalyzes the metal ion-independent decarboxylation of malonate semialdehyde to produce acetaldehyde and carbon dioxide and a low-level hydration of 2-oxo-3-pentynoate to yield acetopyruvate. The latter activity is not known to be biologically relevant. Previous studies identified Pro-1, Asp-37, and a pair of arginines (Arg-73 and Arg-75) as critical residues in these activities. In terms of pairwise sequence, MSAD from Coryneform bacterium strain FG41 (designated FG41 MSAD) is 38% identical with the Pseudomonas enzyme, including Pro-1 and Asp-37. However, Gln-73 replaces Arg-73, and the second arginine is shifted to Arg-76 by the insertion of a glycine. To determine how these changes relate to the activities of FG41 MSAD, the gene was cloned and the enzyme expressed and characterized. The enzyme has a comparable decarboxylase activity but a significantly reduced hydratase activity. Mutagenesis along with crystal structures of the native enzyme (2.0 Å resolution) and the enzyme modified by a 3-oxopropanoate moiety (resulting from the incubation of the enzyme and 3-bromopropiolate) (2.2 Å resolution) provided a structural basis. The roles of Pro-1 and Asp-37 are likely the same as those proposed for Pp MSAD. However, the side chains of Thr-72, Gln-73, and Tyr-123 replace those of Arg-73 and Arg-75 in the mechanism and play a role in binding and catalysis. The structures also show that Arg-76 is likely too distant to play a direct role in the mechanism. FG41 MSAD is the second functionally annotated homologue in the MSAD family of the tautomerase superfamily and could represent a new subfamily.


  • Organizational Affiliation

    Division of Medicinal Chemistry, College of Pharmacy, and ‡Department of Chemistry and Biochemistry, The University of Texas , Austin, Texas 78712-1074, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FG41 Malonate Semialdehyde Decarboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
136coryneform bacteriumMutation(s): 0 
EC: 4.1.1
UniProt
Find proteins for F2Z288 (coryneform bacterium)
Explore F2Z288 
Go to UniProtKB:  F2Z288
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2Z288
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
Q [auth E],
S [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
R [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
R [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.955α = 90
b = 94.692β = 90
c = 190.701γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CaspRmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2014-11-26
    Changes: Other
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description