PDBsum entry: 1mzu

Signaling protein

PDB id: 1mzu

Contents

Protein chains

107 a.a. *

114 a.a. *

108 a.a. *

Ligands

HC4 ×3

Waters ×114

* Residue conservation analysis

PDB id:

1mzu

Name:

Signaling protein

Title:

Crystal structure of the photoactive yellow protein domain from the sensor histidine kinase ppr from rhodospirillum centenum

Structure:

Ppr. Chain: a, b, c. Fragment: n-terminal domain. Engineered: yes

Source:

Rhodospirillum centenum. Organism_taxid: 34018. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.245 R-free: 0.269

Authors:

S.Rajagopal,K.Moffat

Key ref:

S.Rajagopal and K.Moffat (2003). Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction. Proc Natl Acad Sci U S A, 100, 1649-1654. PubMed id: 12563032 DOI: 10.1073/pnas.0336353100

Date:

09-Oct-02 Release date: 25-Feb-03

Protein chain

Q9X2W8  (Q9X2W8_RHOCE) -  PPH

Seq: 884 a.a.

Struc: 107 a.a.*

Protein chain

Q9X2W8  (Q9X2W8_RHOCE) -  PPH

Seq: 884 a.a.

Struc: 114 a.a.

Protein chain

Q9X2W8  (Q9X2W8_RHOCE) -  PPH

Seq: 884 a.a.

Struc: 108 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: signal transduction (4 terms)
• Biochemical function: signal transducer activity (2 terms)

DOI no: 10.1073/pnas.0336353100

Proc Natl Acad Sci U S A 100:1649-1654 (2003)

PubMed id: 12563032

Crystal structure of a photoactive yellow protein from a sensor histidine kinase: conformational variability and signal transduction.

S.Rajagopal, K.Moffat.

ABSTRACT

Photoactive yellow protein (E-PYP) is a blue light photoreceptor, implicated in a negative phototactic response in Ectothiorhodospira halophila, that also serves as a model for the Per-Arnt-Sim superfamily of signaling molecules. Because no biological signaling partner for E-PYP has been identified, it has not been possible to correlate any of its photocycle intermediates with a relevant signaling state. However, the PYP domain (Ppr-PYP) from the sensor histidine kinase Ppr in Rhodospirillum centenum, which regulates the catalytic activity of Ppr by blue light absorption, may allow such issues to be addressed. Here we report the crystal structure of Ppr-PYP at 2 A resolution. This domain has the same absorption spectrum and similar photocycle kinetics as full length Ppr, but a blue-shifted absorbance and considerably slower photocycle than E-PYP. Although the overall fold of Ppr-PYP resembles that of E-PYP, a novel conformation of the beta 4-beta 5 loop results in inaccessibility of Met-100, thought to catalyze chromophore reisomerization, to the chromophore. This conformation also exposes a highly conserved molecular surface that could interact with downstream signaling partners. Other structural differences in the alpha 3-alpha 4 and beta 4-beta 5 loops are consistent with these regions playing significant roles in the control of photocycle dynamics and, by comparison to other sensory Per-Arnt-Sim domains, in signal transduction. Because of its direct linkage to a measurable biological output, Ppr-PYP serves as an excellent system for understanding how changes in photocycle dynamics affect signaling by PYPs.

Selected figure(s)

Figure 3.
Fig. 3. Conformation of the 4- 5 loop. Views from below (A) and the side (B) of the 4- 5 loop of Ppr-PYP (red) and E-PYP (blue), after superposition as in Fig. 2B.

Figure 5.
Fig. 5. Chromophore binding pockets. Chain B of Ppr-PYP (red) and E-PYP (blue) after a least-squares superposition of their hydroxycinnamic acid chromophores.

Figures were selected by an automated process.