PDBsum entry: 1s4r

Photosynthesis

PDB id: 1s4r

Contents

Protein chain

125 a.a. *

Ligands

HC4

Waters ×89

* Residue conservation analysis

PDB id:

1s4r

Name:

Photosynthesis

Title:

Structure of a reaction intermediate in the photocycle of pyp extracted by a svd-driven analysis

Structure:

Photoactive yellow protein. Chain: a. Synonym: pyp. Engineered: yes

Source:

Halorhodospira halophila. Organism_taxid: 1053. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.90Å R-factor: 0.242 R-free: 0.259

Authors:

M.Schmidt,R.Pahl,V.Srajer,S.Anderson,Z.Ren,H.Ihee, S.Rajagopal,K.Moffat

Key ref:

M.Schmidt et al. (2004). Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data. Proc Natl Acad Sci U S A, 101, 4799-4804. PubMed id: 15041745 DOI: 10.1073/pnas.0305983101

Date:

17-Jan-04 Release date: 13-Apr-04

Protein chain

P16113  (PYP_HALHA) -  Photoactive yellow protein

Seq: 125 a.a.

Struc: 125 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to stimulus (5 terms)
• Biochemical function: signal transducer activity (3 terms)

DOI no: 10.1073/pnas.0305983101

Proc Natl Acad Sci U S A 101:4799-4804 (2004)

PubMed id: 15041745

Protein kinetics: structures of intermediates and reaction mechanism from time-resolved x-ray data.

M.Schmidt, R.Pahl, V.Srajer, S.Anderson, Z.Ren, H.Ihee, S.Rajagopal, K.Moffat.

ABSTRACT

We determine the number of authentic reaction intermediates in the later stages of the photocycle of photoactive yellow protein at room temperature, their atomic structures, and a consistent set of chemical kinetic mechanisms, by analysis of a set of time-dependent difference electron density maps spanning the time range from 5 micros to 100 ms. The successful fit of exponentials to right singular vectors derived from a singular value decomposition of the difference maps demonstrates that a chemical kinetic mechanism holds and that structurally distinct intermediates exist. We identify two time-independent difference maps, from which we refine the structures of the corresponding intermediates. We thus demonstrate how structures associated with intermediate states can be extracted from the experimental, time-dependent crystallographic data. Stoichiometric and structural constraints allow the exclusion of one kinetic mechanism proposed for the photocycle but retain other plausible candidate kinetic mechanisms.

Selected figure(s)

Figure 2.
Fig. 2. The time dependence of the rSVs. , first rSV; , second rSV; , third rSV; X, fourth rSV; lines: global fit by a sum of three exponentials. Three relaxation times are marked by arrows. (Inset) Magnitude of the SVs, , and autocorrelation (AC), , of rSVs.

Figure 3.
Fig. 3. The chemical, kinetic mechanisms. (A) General chemical, kinetic mechanism that generates three relaxation times. The state IS1 is the first observed intermediate after the illumination of the dark state pG. The activated molecules relax through two ISs, IS2, and IS3, to the dark state pG. The direct path from IS1 to the dark state pG is not considered. (B-E) Subsets of the general scheme compiled by setting certain rate coefficients to 0. (B) S, Irreversible, sequential mechanism. (C) P, Parallel mechanism. (D) DE, Mechanism with a dead end. (E) SP, Semiparallel mechanism.

Figures were selected by an automated process.