5HI8 | pdb_00005hi8

Structure of T-type Phycobiliprotein Lyase CpeT from Prochlorococcus phage P-HM1

• PDB DOI: https://doi.org/10.2210/pdb5HI8/pdb

• Classification: LYASE
• Organism(s): Prochlorococcus phage P-HM1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-11 Released: 2017-01-18 
• Deposition Author(s): Gasper, R., Schwach, J., Frankenberg-Dinkel, N., Hofmann, E.
• Funding Organization(s): Funded by Transfer.NRW: Science-to-Business Pre Seed

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.274 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Distinct Features of Cyanophage-encoded T-type Phycobiliprotein Lyase Phi CpeT: THE ROLE OF AUXILIARY METABOLIC GENES.

Gasper, R., Schwach, J., Hartmann, J., Holtkamp, A., Wiethaus, J., Riedel, N., Hofmann, E., Frankenberg-Dinkel, N.

(2017) J Biological Chem 292: 3089-3098

• PubMed: 28073912 
• DOI: https://doi.org/10.1074/jbc.M116.769703
• Primary Citation Related Structures: 
  5HI8


• PubMed Abstract: 
  

  Auxiliary metabolic genes (AMG) are commonly found in the genomes of phages that infect cyanobacteria and increase the fitness of the cyanophage. AMGs are often homologs of host genes, and also typically related to photosynthesis. For example, the Φ cpeT gene in the cyanophage P-HM1 encodes a putative phycobiliprotein lyase related to cyanobacterial T-type lyases, which facilitate attachment of linear tetrapyrrole chromophores to Cys-155 of phycobiliprotein β-subunits, suggesting that ΦCpeT may also help assemble light-harvesting phycobiliproteins during infection. To investigate this possibility, we structurally and biochemically characterized recombinant ΦCpeT. The solved crystal structure of ΦCpeT at 1.8-Å resolution revealed that the protein adopts a similar fold as the cyanobacterial T-type lyase CpcT from Nostoc sp. PCC7120 but overall is more compact and smaller. ΦCpeT specifically binds phycoerythrobilin (PEB) in vitro leading to a tight complex that can also be formed in Escherichia coli when it is co-expressed with genes encoding PEB biosynthesis ( i.e. ho1 and pebS ). The formed ΦCpeT·PEB complex was very stable as the chromophore was not lost during chromatography and displayed a strong red fluorescence with a fluorescence quantum yield of Φ _F = 0.3. This complex was not directly able to transfer PEB to the host phycobiliprotein β-subunit. However, it could assist the host lyase CpeS in its function by providing a pool of readily available PEB, a feature that might be important for fast phycobiliprotein assembly during phage infection.

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Organizational Affiliation: 
• Protein Crystallography Group.
Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum.
Department of Biology, Division for Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany.
Physiology of Microorganisms Group, Faculty for Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum; Department of Biology, Division for Microbiology, Technical University Kaiserslautern, 67663 Kaiserslautern, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 32.69 kDa 
• Atom Count: 2,389 
• Modeled Residue Count: 272 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna protein	A, B	136	Prochlorococcus phage P-HM1	Mutation(s): 0  Gene Names: cpeT, PHM1_028
UniProt
Find proteins for E3SMK9 (Prochlorococcus phage P-HM1) Explore E3SMK9  Go to UniProtKB:  E3SMK9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.274 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.29	α = 90
b = 61.68	β = 109.77
c = 93.34	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Gasper, R., Schwach, J., Frankenberg-Dinkel, N., Hofmann, E.

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Funding Organization	Location	Grant Number
Funded by Transfer.NRW: Science-to-Business Pre Seed	Germany	300271002

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary