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Ribulose-phoshate binding barrel superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   TIM beta/alpha-barrel [ 51350] (33)
Superfamily:   Ribulose-phoshate binding barrel [ 51366] (6)
Families:   Histidine biosynthesis enzymes [ 51367] (2)
  D-ribulose-5-phosphate 3-epimerase [ 51372]
  Decarboxylase [ 51375] (3)
  Tryptophan biosynthesis enzymes [ 51381] (3)
  NanE-like [ 117362]
  PdxS-like [ 141755]


Superfamily statistics
Genomes (3,193) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 24,368 133,108 73
Proteins 23,622 130,077 72


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process0.000020860.000000000008624Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000000013170.000000000000003734Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000000000083520Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000022920.000000003275Least InformativeDirect
Biological Process (BP)primary metabolic process0.050260.1762Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0000019060Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.000003260.000000009177Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00000000000012930Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.00000000000015140Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00000042390.000000004913Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.0000000000016590Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.014240.000939Moderately InformativeInherited
Biological Process (BP)organophosphate biosynthetic process0.059910.01861Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.017640.00002694Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000000000086780InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0000160.00009345InformativeDirect
Biological Process (BP)amine metabolic process0.000040160.000000000000001925InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.0000640.00001331InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.00000000000008620.000000000000001925InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.0000000010360InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000000020580.0000000001831InformativeDirect
Biological Process (BP)glycosyl compound metabolic process0.29150.01217InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.42920.2992InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.13320.08271InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0034370.02074InformativeInherited
Biological Process (BP)pyrimidine nucleotide biosynthetic process0.0000033920.000000002357Highly InformativeDirect
Biological Process (BP)tryptophan metabolic process0.000075820.00000000001326Highly InformativeDirect
Biological Process (BP)NADP metabolic process00Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process0.000000025650Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.00020920.000000006652Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.0000000000010090.00000000000001079Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process0.00000064230.000000003916Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.00000000079060Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.00000000049780.0000000000001341Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.00000029780.00000000000008578Highly InformativeDirect
Biological Process (BP)glucose 6-phosphate metabolic process0.000000000000053790.000000000000003734Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.0000000060580Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.00023180.00004498Highly InformativeDirect
Biological Process (BP)nucleoside biosynthetic process0.034080.00002587Highly InformativeInherited
Molecular Function (MF)lyase activity0.0000000000014850Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.00000013520.00000000001104InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.0000150.00000936InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.3770.02979InformativeInherited
Molecular Function (MF)hydro-lyase activity0.0047060.000002751InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.000000076120.00001954Highly InformativeDirect
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives00Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses00Highly InformativeDirect
Cellular Component (CC)cytoplasmic part0.13710.02749Least InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000000000008624 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000000000000003734 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0.000000003275 Least Informative Direct
Biological Process (BP) primary metabolic process 0.1762 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000009177 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00002694 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.000939 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000000004913 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.01861 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.00009345 Informative Direct
Biological Process (BP) amine metabolic process 0.000000000000001925 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00001331 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.000000000000001925 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000000001831 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.2992 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.08271 Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.01217 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.02074 Informative Inherited
Biological Process (BP) pyrimidine nucleotide biosynthetic process 0.000000002357 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.00000000001326 Highly Informative Direct
Biological Process (BP) NADP metabolic process 0 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.000000006652 Highly Informative Direct
Biological Process (BP) nucleoside biosynthetic process 0.00002587 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.00000000000001079 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000003916 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.0000000000001341 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.00000000000008578 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0.000000000000003734 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00004498 Highly Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0.0000005125 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.00000000001104 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.000002751 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.00000936 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.02979 Informative Inherited
Molecular Function (MF) transferase activity, transferring pentosyl groups 0.0000000000003605 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00001954 Highly Informative Direct
Molecular Function (MF) racemase and epimerase activity, acting on carbohydrates and derivatives 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, interconverting aldoses and ketoses 0 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.02749 Least Informative Inherited
Cellular Component (CC) plastid 0.000004794 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related c0InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases1InformativeInherited
Enzyme Commission (EC)Aldehyde-lyases1InformativeInherited
Enzyme Commission (EC)Anthranilate synthase0.0000000009889Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Biological processAromatic amino acid biosynthesis0Highly InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Molecular functionCobalt0.00000000005976InformativeDirect
Molecular functionSchiff base0Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011060 SSF51366 Protein matches
Abstract

The ribulose-phosphate binding barrel consists of a parallel beta-sheet barrel fold containing a phosphate-binding site. Several proteins display this fold, including histidine biosynthesis enzymes, tryptophan biosynthesis enzymes, D-ribulose-5-phosphate 3-epimerase, and decarboxylases [PubMed11688714].


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-quality) · 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 36 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 Ribulose-phoshate binding barrel 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 36 hidden Markov models representing the Ribulose-phoshate binding barrel 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]