Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.50 kDa 
• Atom Count: 3109 
• Modelled Residue Count: 333 
• Deposited Residue Count: 334 
• Unique protein chains: 1

3HJZ

The structure of an aldolase from Prochlorococcus marinus

• PDB DOI: 10.2210/pdb3HJZ/pdb

• Classification: TRANSFERASE
• Organism(s): Prochlorococcus marinus str. MIT 9312
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-22 Released: 2009-06-09 
• Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Literature

Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism.

Thompson, L.R., Zeng, Q., Kelly, L., Huang, K.H., Singer, A.U., Stubbe, J., Chisholm, S.W.

(2011) Proc Natl Acad Sci U S A 108: E757-E764

• PubMed: 21844365 
• DOI: 10.1073/pnas.1102164108
• Primary Citation of Related Structures:  
  3HJZ


• PubMed Abstract: 
  

Cyanophages infecting the marine cyanobacteria Prochlorococcus and Synechococcus encode and express genes for the photosynthetic light reactions. Sequenced cyanophage genomes lack Calvin cycle genes, however, suggesting that photosynthetic energy harvested via phage proteins is not used for carbon fixation. We report here that cyanophages carry and express a Calvin cycle inhibitor, CP12, whose host homologue directs carbon flux from the Calvin cycle to the pentose phosphate pathway (PPP). Phage CP12 was coexpressed with phage genes involved in the light reactions, deoxynucleotide biosynthesis, and the PPP, including a transaldolase gene that is the most prevalent PPP gene in cyanophages. Phage transaldolase was purified to homogeneity from several strains and shown to be functional in vitro, suggesting that it might facilitate increased flux through this key reaction in the host PPP, augmenting production of NADPH and ribose 5-phosphate. Kinetic measurements of phage and host transaldolases revealed that the phage enzymes have k(cat)/K(m) values only approximately one third of the corresponding host enzymes. The lower efficiency of phage transaldolase may be a tradeoff for other selective advantages such as reduced gene size: we show that more than half of host-like cyanophage genes are significantly shorter than their host homologues. Consistent with decreased Calvin cycle activity and increased PPP and light reaction activity under infection, the host NADPH/NADP ratio increased two-fold in infected cells. We propose that phage-augmented NADPH production fuels deoxynucleotide biosynthesis for phage replication, and that the selection pressures molding phage genomes involve fitness advantages conferred through mobilization of host energy stores.

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Organizational Affiliation: 

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transaldolase B	A	334	Prochlorococcus marinus str. MIT 9312	Mutation(s): 0  Gene Names: PMT9312_0519, tal, Transaldose B EC: 2.2.1.2
UniProt
Find proteins for Q31C15 (Prochlorococcus marinus (strain MIT 9312)) Explore Q31C15  Go to UniProtKB:  Q31C15

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	Q [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	H [auth A], I [auth A], J [auth A], K [auth A], O [auth A], P [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.755	α = 90
b = 80.376	β = 90
c = 97.866	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-22 
• Released Date: 2009-06-09 
Deposition Author(s): Singer, A.U., Xu, X., Cui, H., Joachimiak, A., Edwards, A.M., Savchenko, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2012-05-23
  Changes: Database references