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Phosphoenolpyruvate/pyruvate domain 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:   Phosphoenolpyruvate/pyruvate domain [ 51621] (7)
Families:   Pyruvate kinase [ 51622]
  Pyruvate phosphate dikinase, C-terminal domain [ 51629]
  Phosphoenolpyruvate carboxylase [ 51632]
  Phosphoenolpyruvate mutase/Isocitrate lyase-like [ 88704] (3)
  HpcH/HpaI aldolase [ 51638] (3)
  Ketopantoate hydroxymethyltransferase PanB [ 89503]
  Mll9387-like [ 159416]


Superfamily statistics
Genomes (3,222) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 23,554 135,666 43
Proteins 23,439 135,429 43


Functional annotation
General category Metabolism
Detailed category Energy

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)single-organism metabolic process0.00000000037510Least InformativeDirect
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process10.7718Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process0.000082140.06879Least InformativeInherited
Biological Process (BP)amide biosynthetic process0.000012920.0007157Moderately InformativeDirect
Biological Process (BP)carbohydrate metabolic process0.00012960Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00023430.00000005674Moderately InformativeDirect
Biological Process (BP)generation of precursor metabolites and energy0.00091520Moderately InformativeDirect
Biological Process (BP)single-organism catabolic process0.35790.0001257Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.36620.5976Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.13590.8094Moderately InformativeInherited
Biological Process (BP)oxidation-reduction process0.076420.2128Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.012530Moderately InformativeInherited
Biological Process (BP)small molecule biosynthetic process0.63520.3795Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.27660.00006976Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000000000070170.00000000000005058InformativeDirect
Biological Process (BP)water-soluble vitamin biosynthetic process0.000000004650.00000000003115InformativeDirect
Biological Process (BP)cellular modified amino acid metabolic process0.0000001640.0000006266InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.00000027310.00003994InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.47831InformativeInherited
Biological Process (BP)lipid catabolic process0.0000016690.002298InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.000000460.7431InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.17160.2719InformativeInherited
Biological Process (BP)fatty acid metabolic process0.32271InformativeInherited
Biological Process (BP)cellular modified amino acid biosynthetic process0.00000000000053010.0000000000001063Highly InformativeDirect
Biological Process (BP)propionate metabolic process0.000000000022950.000000000004266Highly InformativeDirect
Biological Process (BP)glyoxylate metabolic process0.00000000026870.0000000000126Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.0000000010260.000003601Highly InformativeDirect
Biological Process (BP)fermentation0.000012230.00005656Highly InformativeDirect
Molecular Function (MF)binding0.67671Least InformativeInherited
Molecular Function (MF)transferase activity0.72470.0004062Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.00000000000011050InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.068880.8011InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups0.0000052420.05088InformativeInherited
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity00Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.0000000000017770.0000000005656Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer0.000000073350.00000007671Highly InformativeDirect

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) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 0.7718 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.06879 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) amide biosynthetic process 0.0007157 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00000005674 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00006976 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0001257 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000000002481 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.00000000002684 Moderately Informative Direct
Biological Process (BP) protein complex biogenesis 0.2541 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.747 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.002415 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.5976 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8094 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.2128 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.05648 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.3795 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01431 Moderately Informative Inherited
Biological Process (BP) animal organ development 1 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.00000000000005058 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00000000003115 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 0.0000006266 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00003994 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000002362 Informative Direct
Biological Process (BP) phosphorylation 0.000007062 Informative Direct
Biological Process (BP) protein oligomerization 0.02253 Informative Inherited
Biological Process (BP) reproductive system development 0.1356 Informative Inherited
Biological Process (BP) post-embryonic development 0.3066 Informative Inherited
Biological Process (BP) single organism reproductive process 1 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) lipid catabolic process 0.002298 Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.009254 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.7431 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.2719 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.7321 Informative Inherited
Biological Process (BP) fatty acid metabolic process 1 Informative Inherited
Biological Process (BP) cellular respiration 1 Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0.2101 Informative Inherited
Biological Process (BP) monosaccharide metabolic process 0.09641 Informative Inherited
Biological Process (BP) cellular modified amino acid biosynthetic process 0.0000000000001063 Highly Informative Direct
Biological Process (BP) propionate metabolic process 0.000000000004266 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0.0000000000126 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.000003601 Highly Informative Direct
Biological Process (BP) fermentation 0.00005656 Highly Informative Direct
Biological Process (BP) glycolytic process 0.000000002556 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.00000001707 Highly Informative Direct
Biological Process (BP) phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0000003806 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.00008773 Highly Informative Direct
Biological Process (BP) seed development 0.0005062 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0.9849 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0004062 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000002847 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.4263 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.2158 Moderately Informative Inherited
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) magnesium ion binding 0.00000002821 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.8011 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.05088 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.1113 Informative Inherited
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 0.0000000005656 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer 0.00000007671 Highly Informative Direct
Molecular Function (MF) carbohydrate transmembrane transporter activity 0.000000001987 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 1 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01016 Least 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) microbody 0.0002027 Informative Direct
Cellular Component (CC) plastid 0.0001335 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00008694 Highly 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)Transferring one-carbon groups0Least InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as accep0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a nitrogenous group as ac0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.00002387InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.259InformativeInherited
Enzyme Commission (EC)Phosphoenolpyruvate--protein phosphotransferase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate kinase0Highly InformativeDirect
Enzyme Commission (EC)Pyruvate, phosphate dikinase0.000000008653Highly InformativeDirect
Enzyme Commission (EC)Pyruvate, water dikinase0.000000734Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processGlycolysis0InformativeDirect
Biological processAromatic hydrocarbons catabolism0.00000000001988InformativeDirect
Biological processPhosphotransferase system0Highly InformativeDirect
Biological processSugar transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionPotassium0InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015813 SSF51621 Protein matches
Abstract

Pyruvate kinase controls the exit from the glysolysis pathway, catalysing the transfer of phosphate from phosphooenolpyruvate (PEP) to ADP. Mammalian pyruvate kinase is a homotetramer, where each polypeptide subunit consists of four domains: N-terminal, A domain, B domain and C-terminal. Activation of the enzyme is believed to occur via the clamping down of the B domain onto the A domain to dehydrate the active site cleft. The N- and C-terminal domains are situated at inter-subunit contact sites, and could be involved in assembly and communication within the complex. The N-terminal domain has a TIM beta/alpha-barrel structure. Homologous TIM-barrel domains are found in the following proteins:

  • N-terminal of pyruvate kinase , which is interrupted by an all-beta domain [PubMed11563914].
  • C-terminal of pyruvate phosphate dikinase , which has a similar mode of substrate binding to pyruvate kinase [PubMed11790099].
  • Phosphoenolpyruvate carboxylase ; this domain has additional helices [PubMed12467579].
  • Phosphenolpyruvate mutase/Isocitrate lyase , where it forms a swapped dimer [PubMed11526312].
  • HpcH/HpaI aldolases, such as the beta subunit of citrate lyase, where it forms a swapped dimer, and contains a pyruvate kinase-type metal binding site [PubMed7064730].
  • Ketopantoate hydroxymethyltransferase PanB , where a C-terminal helix exchange is observed in some enzymes [PubMed12906829].

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 24 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 Phosphoenolpyruvate/pyruvate 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 24 hidden Markov models representing the Phosphoenolpyruvate/pyruvate 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]