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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 (3,190) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,340 145,831 73
Proteins 23,594 141,626 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 process0.000023720.000000000008871Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000000015340.000000000000003764Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000000000090760Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.0000019510.000000002935Least InformativeDirect
Biological Process (BP)primary metabolic process0.050570.1727Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0000022060Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.0000033340.00000001063Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.00000000000013520Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.00000000000014910Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.00000040380.000000004109Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.0000000000016040Moderately InformativeDirect
Biological Process (BP)organophosphate biosynthetic process0.060110.01993Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.018080.00002835Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.016430.001085Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000000000094160InformativeDirect
Biological Process (BP)amine metabolic process0.000046710.000000000000001945InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.000057590.00001535InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process0.0000000000007720.0000000000001404InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.0000000010490InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000000018950.0000000001732InformativeDirect
Biological Process (BP)glycosyl compound metabolic process0.28880.01224InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.1320.08436InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.43020.2972InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0032780.02051InformativeInherited
Biological Process (BP)pyrimidine nucleotide biosynthetic process0.0000039920.000000002812Highly InformativeDirect
Biological Process (BP)tryptophan metabolic process0.00008010.00000000001757Highly InformativeDirect
Biological Process (BP)NADP metabolic process00Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process0.00000002420Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.00019540.000000006115Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.0000000000011890.00000000000001615Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process0.00000057680.000000003818Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.00000000090480Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.0000000005930.000000000000187Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.00000026460.00000000000008994Highly InformativeDirect
Biological Process (BP)glucose 6-phosphate metabolic process0.000000000000064040.000000000000005614Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.000000007070Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.00025430.00005185Highly InformativeDirect
Biological Process (BP)nucleoside biosynthetic process0.029310.00002381Highly InformativeInherited
Molecular Function (MF)lyase activity0.0000000000014880Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.00000016110.0000000000114InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.000013840.000007877InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.38470.03182InformativeInherited
Molecular Function (MF)hydro-lyase activity0.0046270.000003073InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.000000071310.00001761Highly 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 part0.13580.02737Least 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 0.000000000008871 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 0.000000000000003764 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 0.000000002935 Least Informative Direct
Biological Process (BP) primary metabolic process 0.1727 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.00000001063 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 0.00002835 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.000000004109 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate biosynthetic process 0.01993 Moderately Informative Inherited
Biological Process (BP) cofactor metabolic process 0.001085 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) amine metabolic process 0.000000000000001945 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00001535 Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0.0000000000001404 Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000000001732 Informative Direct
Biological Process (BP) glycosyl compound metabolic process 0.01224 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.08436 Informative Inherited
Biological Process (BP) water-soluble vitamin biosynthetic process 0.2972 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.02051 Informative Inherited
Biological Process (BP) pyrimidine nucleotide biosynthetic process 0.000000002812 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.00000000001757 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 0.000000006115 Highly Informative Direct
Biological Process (BP) nucleoside biosynthetic process 0.00002381 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.00000000000001615 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000003818 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.000000000000187 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.00000000000008994 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0.000000000000005614 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00005185 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 0.0000005093 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000000114 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.000003073 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.000007877 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.03182 Informative Inherited
Molecular Function (MF) transferase activity, transferring pentosyl groups 0.0000000000004164 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00001761 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 0.02737 Least Informative Inherited
Cellular Component (CC) plastid 0.000005924 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

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo0Least InformativeDirect
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)cell0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)ectoderm0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)visual system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)endomesoderm0InformativeDirect

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)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases1Moderately InformativeInherited
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Carbon-nitrogen lyases0.6002InformativeInherited
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses0Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases1Highly InformativeInherited
Enzyme Commission (EC)Oxo-acid-lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAmino-acid biosynthesis0Moderately InformativeDirect
Biological processCarbohydrate metabolism0Moderately InformativeDirect
Biological processAromatic amino acid biosynthesis0Highly InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Biological processPyrimidine biosynthesis0Highly InformativeDirect
Molecular functionCobalt0.00000000004902InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionSchiff base0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0Moderately InformativeDirect
UniPathway (UP)amine and polyamine metabolism0.0003434Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis1Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)one-carbon metabolism1Moderately InformativeInherited
UniPathway (UP)L-histidine biosynthesis0InformativeDirect
UniPathway (UP)UMP biosynthesis via de novo pathway0InformativeDirect
UniPathway (UP)amino-sugar metabolism0InformativeDirect
UniPathway (UP)tryptophan metabolism0InformativeDirect
UniPathway (UP)amine and polyamine degradation0InformativeDirect
UniPathway (UP)aromatic amino-acid biosynthesis0InformativeDirect
UniPathway (UP)L-tryptophan biosynthesis0Highly InformativeDirect
UniPathway (UP)N-acetylneuraminate degradation0Highly InformativeDirect
UniPathway (UP)L-ascorbate degradation0.0001287Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]