3MYP | pdb_00003myp

Crystal structure of tagatose-1,6-bisphosphate aldolase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3MYP/pdb

• Classification: LYASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-10 Released: 2011-01-26 
• Deposition Author(s): Lee, S.J., Kim, H.S., Kim, D.J., Yoon, H.J., Kim, K.H., Yoon, J.Y., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.241 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structures of LacD from Staphylococcus aureus and LacD.1 from Streptococcus pyogenes: Insights into substrate specificity and virulence gene regulation

Lee, S.J., Kim, H.S., Kim, D.J., Yoon, H.J., Kim, K.H., Yoon, J.Y., Suh, S.W.

(2011) FEBS Lett 585: 307-312

• PubMed: 21192932 
• DOI: https://doi.org/10.1016/j.febslet.2010.12.038
• Primary Citation Related Structures: 
  3MYO, 3MYP


• PubMed Abstract: 
  

  Staphylococcus aureus LacD, a Class I tagatose-1,6-bisphosphate (TBP) aldolase, shows broadened substrate specificity by catalyzing the cleavage of 1,6-bisphosphate derivatives of D-tagatose, D-fructose, D-sorbose, and D-psicose. LacD.1 and LacD.2 are two closely-related Class I TBP aldolases in Streptococcus pyogenes. Here we have determined the crystal structures of S. aureus LacD and S. pyogenes LacD.1. Monomers of both enzymes are folded into a (β/α)(8) barrel and two monomers associate tightly to form a dimer in the crystals. The structures suggest that the residues E189 and S300 of rabbit muscle Class I fructose-1,6-bisphosphate (FBP) aldolase are important for substrate specificity. When we mutated the corresponding residues of S. aureus LacD, the mutants (L165E, L275S, and L165E/L275S) showed enhanced substrate specificity toward FBP.

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Organizational Affiliation: 
• Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 151.78 kDa 
• Atom Count: 10,232 
• Modeled Residue Count: 1,284 
• Deposited Residue Count: 1,336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tagatose 1,6-diphosphate aldolase	A, B, C, D	334	Staphylococcus aureus subsp. aureus COL	Mutation(s): 0  Gene Names: lacD, SACOL2183 EC: 4.1.2.40
UniProt
Find proteins for Q5HE13 (Staphylococcus aureus (strain COL)) Explore Q5HE13  Go to UniProtKB:  Q5HE13

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.241 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.899	α = 90
b = 104.899	β = 90
c = 115.863	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Lee, S.J., Kim, H.S., Kim, D.J., Yoon, H.J., Kim, K.H., Yoon, J.Y., Suh, S.W.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary