SUPERFAMILY 1.75 HMM library and genome assignments server


ROP protein superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   ROP-like [ 47379] (8)
Superfamily:   ROP protein [ 47380]
Families:   ROP protein [ 47381]


Superfamily statistics
Genomes (33) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 41 0 7
Proteins 41 0 7


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

InterPro annotation
Cross references IPR000769 SSF47380 Protein matches
Abstract

The Rop protein regulates plasmid DNA replication by modulating the initiation of transcription of the primer RNA precursor. Processing of the precursor, RNAII, is inhibited by hydrogen bonding of RNAII to its complementary sequence in RNAI. Rop increases the affinity of RNAI for RNAII and thus decreases the rate of replication initiation events. The 3D structure of Rop has been determined by X-ray crystallography and refined to 1.7A resolution. The 63 amino acid protein is a homodimer, each monomer consisting almost entirely of two alpha-helices, the whole molecule forming a highly regular four-alpha-helix bundle [PubMed3681971]. This can be approximated by a four-stranded rope, with radius 7.0 A, a left-handed helical twist, and pitch 172.5 A. A very compact packing of side chains in the helix interfaces of the Rop coiled-coil structure is presumed to account for its high stability [PubMed1841691]. The overall details of the structure have been confirmed by proton NMR [PubMed1841691, PubMed2223771].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 3 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a ROP protein domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 3 hidden Markov models representing the ROP protein superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Internal database links ]