SUPERFAMILY 1.75 HMM library and genome assignments server


Pyrimidine nucleoside phosphorylase C-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   alpha/beta-Hammerhead [ 54664] (5)
Superfamily:   Pyrimidine nucleoside phosphorylase C-terminal domain [ 54680]
Families:   Pyrimidine nucleoside phosphorylase C-terminal domain [ 54681] (2)


Superfamily statistics
Genomes (1,434) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,523 11,324 3
Proteins 1,523 11,324 3


Functional annotation
General category Metabolism
Detailed category Coenzyme metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) transferase activity 2.73e-07 Least Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 8.109e-13 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acce0.09686InformativeInherited
Enzyme Commission (EC)Thymidine phosphorylase0Highly InformativeDirect
Enzyme Commission (EC)Pyrimidine-nucleoside phosphorylase1.084e-12Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Glycosyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Pentosyltransferases0InformativeDirect
Enzyme Commission (EC)Phosphotransferases with a phosphate group as acceptor0.08341InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationGlycosyltransferase0InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)metabolic intermediate biosynthesis0.9969Moderately InformativeInherited
UniPathway (UP)nucleotide biosynthesis0InformativeDirect
UniPathway (UP)dTMP biosynthesis0Highly InformativeDirect
UniPathway (UP)pyrimidine salvage0Highly InformativeDirect
UniPathway (UP)5-phospho-alpha-D-ribose 1-diphosphate biosynthesis2.12e-06Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR013102 SSF54680 Protein matches
Abstract

This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [PubMed9817849, PubMed2199449]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, ) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, ) [PubMed9817849]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [PubMed9817849].


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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 Pyrimidine nucleoside phosphorylase 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 Pyrimidine nucleoside phosphorylase 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) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]