SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


PAP/Archaeal CCA-adding enzyme, C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   PAP/Archaeal CCA-adding enzyme, C-terminal domain [ 55003] (2)
Families:   Poly(A) polymerase, PAP, C-terminal domain [ 55004]
  Archaeal tRNA CCA-adding enzyme [ 102995]


Superfamily statistics
Genomes (657) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,520 3,476 8
Proteins 1,520 3,468 8


Functional annotation
General category Information
Detailed category Transcription

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0.000000000001344 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000001659 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000006495 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000001199 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.000000008898 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001595 Least Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0.000208 Moderately Informative Direct
Biological Process (BP) mRNA processing 0 Highly Informative Direct
Molecular Function (MF) transferase activity 0.00000000001902 Least Informative Direct
Molecular Function (MF) binding 0.1928 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.00001489 Moderately Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0 Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.006038 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.1199 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0008481 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.01429 Moderately Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)CCA tRNA nucleotidyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Polynucleotide adenylyltransferase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processmRNA processing0InformativeDirect
Biological processtRNA processing0InformativeDirect
Cellular componentNucleus0.000000003716Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionManganese0.00000001966Moderately InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationRNA-binding0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011068 SSF55003 Protein matches
Abstract

Nucleotidytransferases can be divided into two classes based on highly conserved features of the nucleotidyltransferase motif [PubMed8809016]. Class I enzymes include eukaryotic poly(A) polymerase (PAP), archaeal tRNA CCA-adding enzyme and possibly DNA polymerase beta, while class II enzymes include eukaryotic and eubacterial tRNA CCA-adding enzymes. This entry represents the C-terminal domain of class I nucleotidyltransferases. The C-terminal domain has an alpha/beta sandwich fold, although the archaeal tRNA CCA-adding enzyme has a large insertion; this fold is reminiscent of the RNA-recognition motif fold.

Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. The catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase [PubMed10944102]. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase.

The archaeal CCA-adding enzyme builds and repairs the 3 ' end of tRNA. A single active site (nucleotidyltransferase motif) adds both CTP and ATP [PubMed15590678]. This enzyme is the only RNA polymerase that can build or rebuild a specific nucleic acid sequence without using a nucleic acid template.


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 · Gene Ontology (high-coverage) · 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 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 PAP/Archaeal CCA-adding enzyme, C-terminal 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 3 hidden Markov models representing the PAP/Archaeal CCA-adding enzyme, C-terminal 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 · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]