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Rop protein

From Proteopedia

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Function

(Repressor Of Primer) is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded^[1]. Its structure has been studied using both X-ray crystallography^[2] and NMR^[3]. Each monomer has molecular weight of about 7.500 Da and it consists of 63 amino acids that form two α-helices connected by of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis.

4-α-helical bundle

Rop is the paradigm of a canonical 4-α-helical bundle and its apparent structural simplicity of its folding rendered it as a model system for investigating the sequence-structure relationships in the folding and dynamics of 4-α-helix. The four α-helices are amphipathic, packed in an antiparallel fashion and display a specific pattern of hydrophobic and hydrophilic amino acids, of the type (a,b,c,d,e,f,g)n, which is repeated every seven residues (heptad pattern). Positions a and d are generally hydrophobic and the side chains of these residues are packed in the central part of the structure according to the “knobs in holes” model forming the hydrophobic core. The heptad periodicity in the sequence of Rop is disrupted only once and leads to the formation of the loop. has a crucial role in the formation of the loop region as it is the only amino acid that simultaneously forms hydrogen bond to both helices.

Mutants

Numerous mutations in the loop region of Rop have been produced:

deletion of 5 a/a of loop (1qx8)
site-directed mutants in loop
replacement and insertion of glycine residues in loop
restored of heptad pattern in loop region) (1nkd)
a single alanine to proline substitution (1b6q) (Pro31, unlike Ala31, is more confor-mationally constrained, the dihedral angles of Ala31 in the wild type molecule are prohibited to Pro, and leads to a folding pathway for a thermodynamically less stable conformation.)
re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle(1yo7)
ALA2ILE2-6, repacted the hydrophobic core and a new fold (1f4n)

3D structures of Rop protein

Updated on 09-March-2022

1rpo, 1rop, 2ghy – EcRop – Escherichia coli
1qx8, 1nkd, 1b6q, 1yo7, 1f4n, 3k79, 2ijh, 2iji, 2ijj, 2ijk, 1gmg, 1f4m, 4do2, 1gto, 7kae – EcRop (mutant)
1rpr – EcRop – NMR
3q5z – TgRop5B pseudokinase domain – Toxoplasma gondii
3q60 – TgRop5B pseudokinase domain + ATP

Additional Resources

For additional information, see: DNA Replication, Repair, and Recombination

References

↑ Polisky B. ColE1 replication control circuitry: sense from antisense. Cell. 1988 Dec 23;55(6):929-32. PMID:2462471
↑ Banner DW, Kokkinidis M, Tsernoglou D. Structure of the ColE1 rop protein at 1.7 A resolution. J Mol Biol. 1987 Aug 5;196(3):657-75. PMID:3681971
↑ Eberle W, Pastore A, Sander C, Rosch P. The structure of ColE1 rop in solution. J Biomol NMR. 1991 May;1(1):71-82. PMID:1841691

Proteopedia Page Contributors and Editors (what is this?)

Maria Amprazi, Michal Harel, Nicole R Pendini, Alexander Berchansky, Keith Callenberg, Jaime Prilusky, David Canner

Retrieved from "http://52.214.119.220/wiki/index.php/Rop_protein"

Category: Topic Page

@@ Line 1: / Line 1: @@
-{{STRUCTURE_1rop |  PDB=1rop  |  SCENE=Rop_protein/Wt_rop/1 caption=E. Coli Rop protein ({DB code [[1rop]])}}<scene name='Rop_protein/Wt_rop/1'>Rop</scene> '''(Repressor Of Primer)''' is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>pmid 2462471</ref>. Its structure has been studied using both X-ray crystallography (Banner ''et al.'', 1987) and NMR (Eberle ''et al''., 1991).
+<StructureSection load='1rop' size='350' side='right' scene='' caption='E. coli Rop protein [[1rop]]'>
+==Function==
+<scene name='Rop_protein/Wt_rop/1'>Rop</scene> '''(Repressor Of Primer)''' is a small homodimeric RNA-binding protein that is involved in the regulation of copy number of the ColE1 plasmids of E.coli, where it is encoded<ref>pmid 2462471</ref>. Its structure has been studied using both X-ray crystallography<ref>PMID:3681971</ref> and NMR<ref>PMID:1841691</ref>.
 Each monomer has molecular weight of about 7.500 Da and it consists of 63 amino acids that form two α-helices connected by <scene name='Rop_protein/Wt_rop_loop/2'> a loop </scene>of four amino acids (L29, D30, A31, D32). The two monomers are related with a 2-fold symmetry axis.
@@ Line 14: / Line 17: @@
 *re-engineering topology of the homodimeric ROP protein into a single-chain 4-helix bundle([[1yo7]])
 *ALA2ILE2-6, repacted the hydrophobic core and a new fold ([[1f4n]])
+</StructureSection>
 ==3D structures of Rop protein==
@@ Line 20: / Line 23: @@
 [[1rpo]], [[1rop]], [[2ghy]] – EcRop – ''Escherichia coli''<br />
-[[1qx8]], [[1nkd]], [[1b6q]], [[1yo7]], [[1f4n]], [[3k79]], [[2ijh]], [[2iji]], [[2ijj]], [[2ijk]], [[1gmg]], [[1f4m]], [[4do2]] – EcRop (mutant)<br />
+[[1qx8]], [[1nkd]], [[1b6q]], [[1yo7]], [[1f4n]], [[3k79]], [[2ijh]], [[2iji]], [[2ijj]], [[2ijk]], [[1gmg]], [[1f4m]], [[4do2]], [[1gto]], [[7kae]] – EcRop (mutant)<br />
 [[1rpr]] – EcRop – NMR<br />
 [[3q5z]] – TgRop5B pseudokinase domain – ''Toxoplasma gondii'' <br />

Rop protein

From Proteopedia

Current revision

Function

4-α-helical bundle

Mutants

3D structures of Rop protein

Additional Resources

References

Proteopedia Page Contributors and Editors (what is this?)

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