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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 (3,184) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 24,306 145,831 73
Proteins 23,562 141,626 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 process0.00000000000068590Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.000000000042880Least InformativeDirect
Biological Process (BP)biosynthetic process0.000033720.00000000002111Least InformativeDirect
Biological Process (BP)single-organism metabolic process0.000000000076780Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000000000000032580Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000000018660Least InformativeDirect
Biological Process (BP)cellular amino acid metabolic process0.000031580.00000000000002447Moderately InformativeDirect
Biological Process (BP)phosphate-containing compound metabolic process0.00000028090.00000005099Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.000000000056690Moderately InformativeDirect
Biological Process (BP)aromatic compound biosynthetic process0.00000002150.0000000000006688Moderately InformativeDirect
Biological Process (BP)organophosphate metabolic process0.00036450.00001601Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.00000013530.00000000000006543Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process0.0000044190.00000000004633Moderately InformativeDirect
Biological Process (BP)cofactor metabolic process0.000062160.00001447Moderately InformativeDirect
Biological Process (BP)organic cyclic compound biosynthetic process0.00000000039290Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.0000000035740Moderately InformativeDirect
Biological Process (BP)carbohydrate derivative metabolic process0.61050.1967Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.00065760.002274Moderately InformativeInherited
Biological Process (BP)nucleobase-containing small molecule metabolic process0.0022150.00001849Moderately InformativeInherited
Biological Process (BP)organic hydroxy compound metabolic process0.014040.06712Moderately InformativeInherited
Biological Process (BP)cellular biogenic amine metabolic process0.00000000028090InformativeDirect
Biological Process (BP)oxidoreduction coenzyme metabolic process0.0000019280.0000149InformativeDirect
Biological Process (BP)vitamin metabolic process0.00030390.0002025InformativeDirect
Biological Process (BP)carbohydrate catabolic process0.0000000000079220.0000000000004323InformativeDirect
Biological Process (BP)ribose phosphate biosynthetic process0.00031140.00000001529InformativeDirect
Biological Process (BP)pyridine-containing compound metabolic process00InformativeDirect
Biological Process (BP)pyrimidine-containing compound metabolic process0.00022820.00000000000007337InformativeDirect
Biological Process (BP)alpha-amino acid biosynthetic process0.00000064710.000000003753InformativeDirect
Biological Process (BP)glycosyl compound biosynthetic process0.074610.0008002InformativeInherited
Biological Process (BP)nucleotide biosynthetic process0.75810.08588InformativeInherited
Biological Process (BP)nucleoside monophosphate metabolic process0.66220.9897InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.0056620.0406InformativeInherited
Biological Process (BP)hexose metabolic process0.063430.1446InformativeInherited
Biological Process (BP)tryptophan metabolic process0.00038230.0000000001341Highly InformativeDirect
Biological Process (BP)aromatic amino acid family biosynthetic process0.000000032940Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process00Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.00000027020Highly InformativeDirect
Biological Process (BP)vitamin B6 metabolic process0.0000055990.00000005105Highly InformativeDirect
Biological Process (BP)pyrimidine ribonucleoside metabolic process0.00000041710.000000000000001931Highly InformativeDirect
Biological Process (BP)nicotinamide nucleotide metabolic process00Highly InformativeDirect
Biological Process (BP)imidazole-containing compound metabolic process0.000000004290.00000000000003117Highly InformativeDirect
Biological Process (BP)pyridine-containing compound biosynthetic process0.000003080.0000002022Highly InformativeDirect
Biological Process (BP)pyrimidine-containing compound biosynthetic process0.000033960.0000000000008893Highly InformativeDirect
Biological Process (BP)nucleobase metabolic process0.0046090.0000007737Highly InformativeInherited
Biological Process (BP)pyrimidine nucleotide metabolic process0.030180.000002389Highly InformativeInherited
Biological Process (BP)nucleoside monophosphate biosynthetic process0.0031080.000002755Highly InformativeInherited
Molecular Function (MF)lyase activity0.000000020120Moderately InformativeDirect
Molecular Function (MF)isomerase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.000081540.0000000006727InformativeDirect
Molecular Function (MF)hydro-lyase activity0.00077410.0000003163InformativeDirect
Molecular Function (MF)racemase and epimerase activity0.000012610.000002335InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity0.52810.05505InformativeInherited
Molecular Function (MF)racemase and epimerase activity, acting on carbohydrates and derivatives00Highly InformativeDirect
Molecular Function (MF)intramolecular oxidoreductase activity, interconverting aldoses and ketoses00Highly InformativeDirect
Molecular Function (MF)carboxy-lyase activity0.00016570.001611Highly InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle11Least InformativeInherited
Cellular Component (CC)cytoplasmic part0.24960.01699Least InformativeInherited
Cellular Component (CC)plastid0.0025210.0000007997InformativeInherited

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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000000002111 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 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) cellular amino acid metabolic process 0.00000000000002447 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00000005099 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.0000000000006688 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00001601 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.00000000000006543 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0.00000000004633 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00001447 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00001849 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.002274 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.1967 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.06712 Moderately Informative Inherited
Biological Process (BP) cellular biogenic amine metabolic process 0 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.0000149 Informative Direct
Biological Process (BP) vitamin metabolic process 0.0002025 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000000000004323 Informative Direct
Biological Process (BP) ribose phosphate biosynthetic process 0.00000001529 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) pyrimidine-containing compound metabolic process 0.00000000000007337 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.000000003753 Informative Direct
Biological Process (BP) glycosyl compound biosynthetic process 0.0008002 Informative Direct
Biological Process (BP) nucleotide biosynthetic process 0.08588 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.9897 Informative Inherited
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0406 Informative Inherited
Biological Process (BP) hexose metabolic process 0.1446 Informative Inherited
Biological Process (BP) pyrimidine nucleotide metabolic process 0.000002389 Highly Informative Direct
Biological Process (BP) tryptophan metabolic process 0.0000000001341 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0 Highly Informative Direct
Biological Process (BP) nucleobase metabolic process 0.0000007737 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate biosynthetic process 0.000002755 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0 Highly Informative Direct
Biological Process (BP) vitamin B6 metabolic process 0.00000005105 Highly Informative Direct
Biological Process (BP) pyrimidine ribonucleoside metabolic process 0.000000000000001931 Highly Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.00000000000003117 Highly Informative Direct
Biological Process (BP) pyridine-containing compound biosynthetic process 0.0000002022 Highly Informative Direct
Biological Process (BP) pyrimidine-containing compound biosynthetic process 0.0000000000008893 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 0.0000000003536 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000000006727 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.0000003163 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.000002335 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.05505 Informative Inherited
Molecular Function (MF) transferase activity, transferring pentosyl groups 0 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
Molecular Function (MF) carboxy-lyase activity 0.001611 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01699 Least Informative Inherited
Cellular Component (CC) plastid 0.0000007997 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

Yeast Phenotype (YP)

(show details) Document: YP 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)Carboxy-lyases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases1InformativeInherited
Enzyme Commission (EC)Acting on carbohydrates and derivatives0Highly InformativeDirect
Enzyme Commission (EC)Interconverting aldoses and ketoses, and related compounds0Highly 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 functionCobalt0.0000000002177InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationDecarboxylase0InformativeDirect

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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]