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G-protein coupled receptor homology

Overall sequence homology in GPCR family

- families of GPCR with no sequence homology Bockaert, J. and J.P. Pin, Molecular tinkering of G protein-coupled receptors: an evolutionary success. Embo J, 1999. 18(7): p. 1723-9

- "GPCR do NOT share any overall sequence homology" and "the only structural feature common to all GPCRs is the presence of TM helices" (Gether (2000) review, he gives references: 

    Kolakowski, L.F., Jr., GCRDb: a G-protein-coupled receptor database. Receptors Channels, 1994. 2(1): p. 1-7.

        and

    Probst, W.C., L.A. Snyder, D.I. Schuster, J. Brosius, and S.C. Sealfon, Sequence alignment of the G-protein coupled receptor superfamily. DNA Cell Biol, 1992. 11(1): p. 1-20.

- significant sequence homology found in subfamilies - A B C D E (Gether, 2000)

 

Horn, F., J. Weare, M.W. Beukers, S. Horsch, A. Bairoch, W. Chen, O. Edvardsen, F. Campagne, and G. Vriend, GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res, 1998. 26(1): p. 275-9

the organization into classes is originally based on the pharmacological classification of receptors

classes share > 20% sequence identity over predicted transmembrane helices

Multiple sequence alignment designed specifically for GPCR based on WHAT IF (using neighbor-joining algorithm): ref. Oliveira, L., A.C. Paiva, and G. Vriend, J Comp.-Aid. Mol. Des., 1993. 7(649-648)

In this method, the sequences are numbered such that 100s digits indicate the helix number and the most conserved residue in every helix has a round number. However, we found that this is sometimes wrong and parts of the sequence got 100s numbers that are not TM helices.

 

Hermans, E. and R.A. Challiss, Structural, signalling and regulatory properties of the group I metabotropic glutamate receptors: prototypic family C G-protein-coupled receptors. Biochem J, 2001. 359(Pt 3): p. 465-84

- general properties of Class C:

    mGluR, GABAB (3 subtypes gamma-aminobutyric acid), extracellular calcium-sensing receptor CaR and a broad multigene family of olfactory, taste and pheromone recpetors

    within TM domains family C share 10-15% amino acid identity with family A/B members

    all family C  have large EC domain (usually more than 500 aa)

 

What is conserved in each family? (Gether, 2000 review)

- Family A: 

        the only residue conserved among all family A is Arg in DRY motif

        fingerprint of the rhodopsin subfamily (see Huang et al (2001) introduction):

            DRY in TM III

            N1.50 in TM I

            D2.50 in TM II

            W4.50 in TM IV

            P5.50, P6.50, P7.50 in TM V-VII

- Family B: 

        the only feature similar to family A is the disulfide bond connecting the E-II and E-III

        the D/E R Y motif is ABSENT in Class B

        conserved Prolines are different from those in Class A!!

        most prominent: large ~100 aa long EC N-terminus containing several Cys that are believed to make a network of disulifde bridges (Ulrich, C.D., 2nd, M. Holtmann, and L.J. Miller, Secretin and vasoactive intestinal peptide receptors: members of a unique family of G protein-coupled receptors. Gastroenterology, 1998. 114(2): p. 382-97.)

- Family C: 

        very long N-terminus 500-600 aa

        also shares the two cysteines that are equivalent to Cys110 and Cys187

        the N-term shares remote sequence homology with bacterial periplasmic binding proteins PBPs especially with the Leu/Ile/Val binding protein  (O'Hara, P.J., P.O. Sheppard, H. Thogersen, D. Venezia, B.A. Haldeman, V. McGrane, K.M. Houamed, C. Thomsen, T.L. Gilbert, and E.R. Mulvihill, The ligand-binding domain in metabotropic glutamate receptors is related to bacterial periplasmic binding proteins. Neuron, 1993. 11(1): p. 41-52. Conn, P.J. and J.P. Pin, Pharmacology and functions of metabotropic glutamate receptors. Annu Rev Pharmacol Toxicol, 1997. 37: p. 205-37.)

        

 

Adrenergic Receptor subtypes (9):

    beta1,2,3

    alpha2A,B,C

    alpha1a,b,d

 

Sequence homology versus structural homology:

For soluble proteins:

    clear structural similarity between proteins with >25% sequence identity (Wilson et al. (2000), Yang and Honig (2000))

    structural divergence increases dramatically <25% sequence identity

    However, structural similarity known for proteins with <10% sequence identity

 

 

Rules on which family and subfamily classification is based?

 

Examples:

Sequence identity between bovine rhodopsin and human dopamine D2 receptor: 19% overall, 25% in TM domain (Ballesteros, Shi and Javitch (2001) Structural mimicry in GPCR: Implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors. Mol. Pharmacology 60, 1-19.)