PDBsum entry: 1otd

Signaling protein

PDB-id: 1otd

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PROCHECK

Protein chains

105 a.a. *

Ligands

HC4 ×4

Waters ×224

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1otd

Name:

Signaling protein

Title:

Strong hydrogen bonds in photoactive yellow protein and their role in its photocycle

Structure:

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

Source:

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

UniProt:

Chains A, B: P16113 (PYP_HALHA)

Seq:

125 a.a.

Struc:

105 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Resolution:

1.25Å

R-factor:

0.171

R-free:

0.215

Authors:

S.Anderson,S.Crosson,K.Moffat

Key ref:

S.Anderson et al. (2004). Short hydrogen bonds in photoactive yellow protein.. Acta Crystallogr D Biol Crystallogr, 60, 1008-1016. [PubMed id: 15159559] [DOI: 10.1107/S090744490400616X]

Date:

21-Mar-03

Release date:

11-May-04

Related entries:

2phy
photoactive yellow protein, dark state (unbleached)
1ota
e46q mutant of photoactive yellow protein, p63 at 295k
1otb
wild type photoactive yellow protein, p63 at 295k
1ote
e46q mutant of photoactive yellow protein, p65 at 110k
1oti
e46q mutant of photoactive yellow protein, p65 at 295k

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Key reference

DOI no: 10.1107/S090744490400616X

Acta Crystallogr D Biol Crystallogr 60:1008-1016 (2004)

PubMed id: 15159559

Short hydrogen bonds in photoactive yellow protein.

S.Anderson, S.Crosson, K.Moffat.

ABSTRACT

Eight high-resolution crystal structures of the ground state of photoactive yellow protein (PYP) solved under a variety of conditions reveal that its chromophore is stabilized by two unusually short hydrogen bonds. Both Tyr42 Oeta and Glu46 Oepsilon are separated from the chromophore phenolate oxygen by less than the sum of their atomic van der Waals radii, 2.6 angstroms. This is characteristic of strong hydrogen bonding, in which hydrogen bonds acquire significant covalent character. The hydrogen bond from the protonated Glu46 to the negatively charged phenolate oxygen is 2.58 +/- 0.01 angstroms in length, while that from Tyr42 is considerably shorter, 2.49 +/- 0.01 angstroms. The E46Q mutant was solved to 0.95 angstroms resolution; the isosteric mutation increased the length of the hydrogen bond from Glx46 to the chromophore by 0.29 +/- 0.01 angstroms to that of an average hydrogen bond, 2.88 +/- 0.01 angstroms. The very short hydrogen bond from Tyr42 explains why mutating this residue has such a severe effect on the ground-state structure and PYP photocycle. The effect of isosteric mutations on the photocycle can be largely explained by the alterations to the length and strength of these hydrogen bonds.

Selected figure(s)

Figure 1.
Figure 1 The ground-state coumaric acid chromophore (pCA) and its binding pocket in wild-type PYP. Hydrogen bonds are shown as dashed lines.

Figure 5.
Figure 5 Difference electron-density maps between wild type and E46Q mutant in space group P6[3] superimposed on the wild-type structure. Red contours denote negative difference electron density and blue denote positive. The entire molecule contoured at ±5 is shown at (a) 110 K and (b) at 295 K. The chromophore-binding pocket contoured at ±4 and ±8 is shown at (c) 110 K and (d) at 295 K.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 1008-1016) copyright 2004.

Figures were selected by an automated process.