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LigT-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   LigT-like [ 55143]
Superfamily:   LigT-like [ 55144] (4)
Families:   tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [ 55145]
  2'-5' RNA ligase LigT [ 89967]
  2',3'-cyclic nucleotide 3'-phosphodiesterase, catalytic domain [ 103043]
  Atu0111-like [ 143484]


Superfamily statistics
Genomes (2,055) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,551 25,272 4
Proteins 3,545 25,235 4


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)Acting on ester bonds0.000000006659Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR009097 SSF55144 Protein matches
Abstract

This entry represents a beta-barrel domain consisting of a duplication of a beta/alpha/beta/alpha/beta motif, which is found in the 2'-5' RNA ligase LigT [PubMed12798681], the tRNA splicing product Appr>p cyclic nucleotide phosphodiesterase [PubMed11694509], and as the catalytic domain in 2',3'-cyclic nucleotide 3'-phosphodiesterase [PubMed17480208]. This beta-barrel domain is similar in structure to the beta-barrel found in prokaryotic DNA topoisomerases I and III.

The 2'-5' RNA ligase family members are bacterial and archaeal RNA ligases that ligate 5' and 3' half-tRNA molecules with 2',3'-cyclic phosphate and 5'-hydroxyl termini, respectively, to the product containing the 2'-5' phosphodiester linkage.

Appr>p cyclic nucleotide phosphodiesterase (CPDase) from Arabidopsis thaliana (Mouse-ear cress) is an enzyme involved in the tRNA splicing pathway. CPDase acts to hydrolyse the tRNA splicing product ADP-ribose 1",2"-cyclic phosphate (Appr>p) to the monoester ADP-ribose 1"-phosphate (Appr-1"p). 2',3'-cyclic uridine vanadate is a putative inhibitor of CPDase. The crystal structure of CPDase reveals a bilobal arrangement of duplicated beta-alpha-beta-alpha-beta motifs, where the antiparallel beta sheet forms a barrel similar to that of prokaryotic DNA topoisomerases I and III [PubMed11080166]. CPDase contains six cysteine residues, four of which form two intramolecular disulphide bridges [PubMed11694509].


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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 11 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 LigT-like 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 11 hidden Markov models representing the LigT-like 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) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]