PDBsum entry 1j7x

Transport protein

PDB id

1j7x

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Contents

			Protein chain

					302 a.a. *

			Waters ×145

* Residue conservation analysis

PDB id:

1j7x

Links

Name:

Transport protein

Title:

Crystal structure of a functional unit of interphotoreceptor retinoid- binding protein (irbp)

Structure:

Interphotoreceptor retinoid-binding protein. Chain: a. Synonym: irbp. Engineered: yes

Source:

Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å

R-factor:

0.207

R-free:

0.220

Authors:

A.Loew,F.Gonzalez-Fernandez

Key ref:

A.Loew and F.Gonzalez-Fernandez (2002). Crystal structure of the functional unit of interphotoreceptor retinoid binding protein. Structure, 10, 43-49. PubMed id: 11796109 DOI: 10.1016/S0969-2126(01)00698-0

Date:

19-May-01

Release date:

20-Feb-02

PROCHECK

	Headers

	References

Protein chain

Q7SZI7 (RET3_XENLA) - Retinol-binding protein 3 from Xenopus laevis

Seq: Struc:

Seq: Struc:

Seq: Struc:					1219 a.a. 302 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

DOI no: 10.1016/S0969-2126(01)00698-0	Structure 10:43-49 (2002)
PubMed id: 11796109

Crystal structure of the functional unit of interphotoreceptor retinoid binding protein.
A.Loew, F.Gonzalez-Fernandez.

ABSTRACT

Interphotoreceptor retinoid binding protein (IRBP), the major soluble component of the interphotoreceptor matrix, is critical to the function, integrity, and development of the vertebrate retina. Although its role is poorly understood, IRBP has been thought to protect 11-cis retinal and all-trans retinol while facilitating their exchange between the photoreceptors and retinal-pigmented epithelium. We determined the X-ray structure of one of the functional units, or modules, of Xenopus laevis IRBP to 1.8 A resolution by multiwavelength anomalous dispersion. The monomeric protein consists of two domains separated by a hydrophobic ligand binding site. A structural homology to the recently solved photosystem II D1 C-terminal-processing protease and the enoyl-CoA isomerase/hydratase family suggests the utility of a common fold used in diverse settings, ranging from proteolysis to fatty acid isomerization to retinoid transport.

Selected figure(s)



	Figure 3. Figure 3. Putative Ligand Binding Sites of X2IRBP(A) Ribbon stereo diagram of X2IRBP (shown in yellow) superposed with 2-enoyl-CoA hydratase (blue) in complex with octanoyl-CoA (red). The bound ligand of 2-enoyl-CoA hydratase was transferred from the 2-enoyl-CoA hydratase/octanoyl-CoA structure to the equivalent position in X2IRBP. The fatty acid portion of the ligand binds to the hydrophobic site 1, as identified in Figure 3b.(B) Hydrophobicity surface representation, where white represents high hydrophobicity and blue high hydrophilicity. The arrowhead identifies a shallow hydrophobic binding cleft between domains A and B, the putative first binding site (site 1). The arrow identifies a cavity located in a hydrophobic patch that leads to the potential second binding site (site 2).

Figure was selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21067480

M.Ksantini, A.Sénéchal, B.Bocquet, I.Meunier, P.Brabet, and C.P.Hamel (2010).
Screening genes of the visual cycle RGR, RBP1 and RBP3 identifies rare sequence variations.

Ophthalmic Genet, 31, 200-204.

20488254

V.C.Fleisch, and S.C.Neuhauss (2010).
Parallel visual cycles in the zebrafish retina.

Prog Retin Eye Res, 29, 476-486.

19074801

A.I.den Hollander, T.L.McGee, C.Ziviello, S.Banfi, T.P.Dryja, F.Gonzalez-Fernandez, D.Ghosh, and E.L.Berson (2009).
A homozygous missense mutation in the IRBP gene (RBP3) associated with autosomal recessive retinitis pigmentosa.

Invest Ophthalmol Vis Sci, 50, 1864-1872.

19388144

D.Chen, J.Chai, P.J.Hart, and G.Zhong (2009).
Identifying catalytic residues in CPAF, a Chlamydia-secreted protease.

Arch Biochem Biophys, 485, 16-23.

18079675

D.Ghosh, J.B.Griswold, T.Bevilacqua, and F.Gonzalez-Fernandez (2007).
Purification of the full-length Xenopus interphotoreceptor retinoid binding protein and growth of diffraction-quality crystals.

Mol Vis, 13, 2275-2281.

17683573

F.Gonzalez-Fernandez, C.A.Baer, and D.Ghosh (2007).
Module structure of interphotoreceptor retinoid-binding protein (IRBP) may provide bases for its complex role in the visual cycle - structure/function study of Xenopus IRBP.

BMC Biochem, 8, 15.

17200656

J.M.Nickerson, R.A.Frey, V.T.Ciavatta, and D.L.Stenkamp (2006).
Interphotoreceptor retinoid-binding protein gene structure in tetrapods and teleost fish.

Mol Vis, 12, 1565-1585.

16847097

P.Ala-Laurila, A.V.Kolesnikov, R.K.Crouch, E.Tsina, S.A.Shukolyukov, V.I.Govardovskii, Y.Koutalos, B.Wiggert, M.E.Estevez, and M.C.Cornwall (2006).
Visual cycle: Dependence of retinol production and removal on photoproduct decay and cell morphology.

J Gen Physiol, 128, 153-169.

16254552

D.L.Stenkamp, J.L.Calderwood, E.E.Van Niel, L.M.Daniels, and F.Gonzalez-Fernandez (2005).
The interphotoreceptor retinoid-binding protein (IRBP) of the chicken (Gallus gallus domesticus).

Mol Vis, 11, 833-845.

13678959

K.D.Ridge, N.G.Abdulaev, M.Sousa, and K.Palczewski (2003).
Phototransduction: crystal clear.

Trends Biochem Sci, 28, 479-487.

14556291

L.L.Cunningham, and F.Gonzalez-Fernandez (2003).
Internalization of interphotoreceptor retinoid-binding protein by the Xenopus retinal pigment epithelium.

J Comp Neurol, 466, 331-342.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.