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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 (3,186) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,324 145,831 73
Proteins 23,578 141,626 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 process0.00003830.00000000001855Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.000000000000038780Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000015890.000000000005579Least InformativeDirect
Biological Process (BP)heterocycle metabolic process00Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000000000027550Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.000000000000019850Least InformativeDirect
Biological Process (BP)primary metabolic process0.10560.2554Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.0000056090Moderately InformativeDirect
Biological Process (BP)nucleoside phosphate metabolic process0.0000014250.000000004963Moderately InformativeDirect
Biological Process (BP)ribose phosphate metabolic process0.00000000000037210Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.02780.002255Moderately InformativeInherited
Biological Process (BP)carbohydrate derivative biosynthetic process0.18190.183Moderately InformativeInherited
Biological Process (BP)glycosyl compound metabolic process10.7129Moderately InformativeInherited
Biological Process (BP)organophosphate biosynthetic process0.044880.01257Moderately InformativeInherited
Biological Process (BP)nucleobase-containing compound biosynthetic process0.26580.5935Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.017340.00002881Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.00000000015570InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.000021810.0001136InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.000027320.000006245InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process0.00000000004060.00000000001197InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.000000040480InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.000000048210.0000000004673InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.52710.1565InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.48610.3294InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0018310.01484InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.1110.06639InformativeInherited
Biological Process (BP)amine metabolic process0.0016370.000000001145InformativeInherited
Biological Process (BP)pyrimidine nucleotide biosynthetic process0.0000013580.0000000011Highly InformativeDirect
Biological Process (BP)tryptophan metabolic process0.000030780.000000000005608Highly InformativeDirect
Biological Process (BP)NADP metabolic process00Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process0.000000015410Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)glyceraldehyde-3-phosphate metabolic process0.0000000000039070.0000000000001129Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process0.00000061120.000000004148Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.0000000010610Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.00000000031970.0000000000005437Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.0000065390.000000000005503Highly InformativeDirect
Biological Process (BP)glucose 6-phosphate metabolic process0.00000000000011160.00000000000003559Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.000000063240.00000000000006455Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.00018610.00003721Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.0079520.00003998Highly InformativeInherited
Molecular Function (MF)lyase activity0.0000000000040570Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.00000032470.00000000002256InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.000039970.00002293InformativeDirect
Molecular Function (MF)hydro-lyase activity0.0030890.000001899InformativeInherited
Molecular Function (MF)intramolecular oxidoreductase activity0.28790.02103InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.000000210.00004285Highly 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 part0.053330.005463Least 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 0.00000000001855 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 0.000000000005579 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 Least Informative Direct
Biological Process (BP) primary metabolic process 0.2554 Least Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000004963 Moderately Informative Direct
Biological Process (BP) ribose phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00002881 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.002255 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative biosynthetic process 0.183 Moderately Informative Inherited
Biological Process (BP) glycosyl compound metabolic process 0.7129 Moderately Informative Inherited
Biological Process (BP) organophosphate biosynthetic process 0.01257 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound biosynthetic process 0.5935 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.0001136 Informative Direct
Biological Process (BP) amine metabolic process 0.000000001145 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.000006245 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.00000000001197 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0000000004673 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.1565 Informative Inherited
Biological Process (BP) water-soluble vitamin biosynthetic process 0.3294 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.01484 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 0.06639 Informative Inherited
Biological Process (BP) pyrimidine nucleotide biosynthetic process 0.0000000011 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.000000000005608 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 0.00003998 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0.0000000000001129 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000004148 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.0000000000005437 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.000000000005503 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0.00000000000003559 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.00000000000006455 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.00003721 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 0.0000003333 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.00000000002256 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.000001899 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.00002293 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.02103 Informative Inherited
Molecular Function (MF) transferase activity, transferring pentosyl groups 0.000000000000361 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.00004285 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 0.005463 Least Informative Inherited
Cellular Component (CC) plastid 0.000001963 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)sensory 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 lyases0.692InformativeInherited
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly 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 functionCobalt0.00000000005097InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionSchiff base0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

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 metabolism0.0003457Moderately 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 degradation0.000131Highly 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 ]