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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 process0.00000000071590Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process10.779Least InformativeInherited
Biological Process (BP)biosynthetic process11Least InformativeInherited
Biological Process (BP)single-organism cellular process0.00010090.02764Least InformativeInherited
Biological Process (BP)organonitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)primary metabolic process11Least InformativeInherited
Biological Process (BP)carbohydrate metabolic process0.00013680Moderately InformativeDirect
Biological Process (BP)generation of precursor metabolites and energy0.00089010Moderately InformativeDirect
Biological Process (BP)monocarboxylic acid metabolic process0.00025260.00000007147Moderately InformativeDirect
Biological Process (BP)amide biosynthetic process0.000016250.0007442Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.63810.3824Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.2920.00008067Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.37350.0001506Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.014190Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.14240.8132Moderately InformativeInherited
Biological Process (BP)lipid metabolic process0.37110.6011Moderately InformativeInherited
Biological Process (BP)oxidation-reduction process0.073720.2121Moderately InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.000000000075350.00000000000006741InformativeDirect
Biological Process (BP)cellular modified amino acid metabolic process0.00000018720.0000007305InformativeDirect
Biological Process (BP)water-soluble vitamin biosynthetic process0.0000000061170.00000000003752InformativeDirect
Biological Process (BP)cellular lipid catabolic process0.00000035890.000002559InformativeDirect
Biological Process (BP)cellular carbohydrate metabolic process0.00000025820.00004064InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.48881InformativeInherited
Biological Process (BP)coenzyme biosynthetic process0.00000059760.7479InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.18050.2775InformativeInherited
Biological Process (BP)fatty acid metabolic process0.33231InformativeInherited
Biological Process (BP)fermentation0.000014180.00005899Highly InformativeDirect
Biological Process (BP)fatty acid catabolic process0.0000000012860.000003536Highly InformativeDirect
Biological Process (BP)propionate metabolic process0.000000000028090.000000000005034Highly InformativeDirect
Biological Process (BP)cellular modified amino acid biosynthetic process0.00000000000070420.0000000000001201Highly InformativeDirect
Biological Process (BP)glyoxylate metabolic process0.00000000028450.00000000001117Highly InformativeDirect
Molecular Function (MF)binding0.72011Least InformativeInherited
Molecular Function (MF)transferase activity0.72220.0003819Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)carbon-carbon lyase activity0.00000000000014490InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups0.065940.7811InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups0.0000056880.05354InformativeInherited
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity00Highly InformativeDirect
Molecular Function (MF)oxo-acid-lyase activity0.0000000000021230.000000000748Highly InformativeDirect
Molecular Function (MF)transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer0.000000084590.00000006505Highly 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) cellular nitrogen compound metabolic process 0.779 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02764 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.00000000002985 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00000007147 Moderately Informative Direct
Biological Process (BP) amide biosynthetic process 0.0007442 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0001506 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.000000000002755 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00008067 Moderately Informative Direct
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.7203 Moderately Informative Inherited
Biological Process (BP) protein complex biogenesis 0.2435 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.3824 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.05666 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.002212 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8132 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.6011 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.01691 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.2121 Moderately Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.00000000000006741 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 0.0000007305 Informative Direct
Biological Process (BP) nucleoside diphosphate metabolic process 0.00000000000004626 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000002361 Informative Direct
Biological Process (BP) phosphorylation 0.000006879 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00000000003752 Informative Direct
Biological Process (BP) cellular lipid catabolic process 0.000002559 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00004064 Informative Direct
Biological Process (BP) ATP metabolic process 0 Informative Direct
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Informative Direct
Biological Process (BP) protein oligomerization 0.02124 Informative Inherited
Biological Process (BP) post-embryonic development 0.3005 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) monosaccharide metabolic process 0.09858 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 0.7479 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.2775 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.7206 Informative Inherited
Biological Process (BP) reproductive system development 0.1367 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 0.2211 Informative Inherited
Biological Process (BP) glucose metabolic process 0.00000002075 Highly Informative Direct
Biological Process (BP) glycolytic process 0.000000002996 Highly Informative Direct
Biological Process (BP) fermentation 0.00005899 Highly Informative Direct
Biological Process (BP) aerobic respiration 0.00009431 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.000003536 Highly Informative Direct
Biological Process (BP) phosphoenolpyruvate-dependent sugar phosphotransferase system 0.0000004035 Highly Informative Direct
Biological Process (BP) propionate metabolic process 0.000000000005034 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0.0000000000001201 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0.00000000001117 Highly Informative Direct
Biological Process (BP) seed development 0.0005621 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0.9848 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0003819 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.000002787 Moderately Informative Direct
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) transporter activity 0.4136 Moderately Informative Inherited
Molecular Function (MF) metal ion binding 0.2585 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.00000002877 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0 Informative Direct
Molecular Function (MF) active transmembrane transporter activity 0.0007213 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.7811 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.1153 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.05354 Informative Inherited
Molecular Function (MF) carbohydrate transmembrane transporter activity 0.000000002065 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) oxo-acid-lyase activity 0.000000000748 Highly Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer 0.00000006505 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 1 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 0.01295 Least Informative Inherited
Cellular Component (CC) plastid 0.0001529 Informative Direct
Cellular Component (CC) microbody 0.0002099 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00009241 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)life span variant0.0002777InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA 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)Transferring phosphorus-containing groups1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Transferring one-carbon groups0Moderately InformativeDirect
Enzyme Commission (EC)Phosphotransferases with an alcohol group as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases0.04133InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a nitrogenous group as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Protein-N(pi)-phosphohistidine--D-fructose phosphotransferase0.00000005576Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.0000001797Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl groups on transfer0.2222Highly InformativeInherited
Enzyme Commission (EC)Aldehyde-lyases0.2924Highly InformativeInherited
Enzyme Commission (EC)Phosphotransferases (phosphomutases)1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processGlycolysis0InformativeDirect
Biological processTricarboxylic acid cycle0InformativeDirect
Biological processAromatic hydrocarbons catabolism0.00000000002045InformativeDirect
Biological processPhosphotransferase system0Highly InformativeDirect
Biological processSugar transport0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentPeroxisome0InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionPotassium0InformativeDirect
Molecular functionPyruvate0Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cofactor metabolism0Least InformativeDirect
UniPathway (UP)carbohydrate metabolism0.000000000002072Least InformativeDirect
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)lipid metabolism1Least InformativeInherited
UniPathway (UP)organic acid metabolism0.00000000000003937Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.0000002297Moderately InformativeDirect
UniPathway (UP)carbohydrate degradation0.03281Moderately InformativeInherited
UniPathway (UP)energy metabolism0.1424Moderately InformativeInherited
UniPathway (UP)carbohydrate biosynthesis1Moderately InformativeInherited
UniPathway (UP)organic acid degradation0InformativeDirect
UniPathway (UP)glycolysis0.00000000008466InformativeDirect
UniPathway (UP)carbohydrate acid metabolism0.0000000008572InformativeDirect
UniPathway (UP)gluconeogenesis0.00008426InformativeDirect
UniPathway (UP)(R)-pantothenate biosynthesis0Highly InformativeDirect
UniPathway (UP)4-hydroxyphenylacetate degradation0Highly InformativeDirect
UniPathway (UP)carbon fixation0Highly InformativeDirect
UniPathway (UP)aldaric acid degradation0Highly InformativeDirect
UniPathway (UP)propanoate degradation0.0000006423Highly InformativeDirect

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