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RNA 3'-terminal phosphate cyclase, RPTC, insert domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Thioredoxin fold [ 52832] (2)
Superfamily:   RNA 3'-terminal phosphate cyclase, RPTC, insert domain [ 52913]
Families:   RNA 3'-terminal phosphate cyclase, RPTC, insert domain [ 52914]


Superfamily statistics
Genomes (422) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 448 0 1
Proteins 448 0 1


Functional annotation
General category Metabolism
Detailed category Other enzymes

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1InformativeInherited

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Forming phosphoric ester bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0.0000000001732Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013791 SSF52913 Protein matches
Abstract

RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. RNA 3'-terminal phosphate cyclase [PubMed9184239, PubMed2199762] catalyses the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA.

ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate

These enzymes might be responsible for production of the cyclic phosphate RNA ends that are known to be required by many RNA ligases in both prokaryotes and eukaryotes.

RNA cyclase is a protein of from 36 to 42 kDa. The best conserved region is a glycine-rich stretch of residues located in the central part of the sequence and which is reminiscent of various ATP, GTP or AMP glycine-rich loops.

The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller insert domain disrupts the large domain, and uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin [PubMed10673421]. Although the active site of this enzyme could not be unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources [PubMed10673421].

This entry represents the small insert domain that interrupts the large repetitive domain.


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

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

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 1 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 RNA 3'-terminal phosphate cyclase, RPTC, insert domain 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 1 hidden Markov models representing the RNA 3'-terminal phosphate cyclase, RPTC, insert domain 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]