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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 (3,224) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 23,592 180,200 43
Proteins 23,477 179,914 43


Functional annotation
General category Metabolism
Detailed category Energy

Document:
Function annotation of SCOP domain superfamilies

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 variant0.0003386Moderately InformativeDirect

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 DEvelopment stage (XDE)post-embryonic stage0Least InformativeDirect
Xenopus DEvelopment stage (XDE)climax stage0Moderately 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)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Thiolester hydrolases0.04919InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Phosphotransferases with a nitrogenous group as acceptor0Highly InformativeDirect
Enzyme Commission (EC)Oxo-acid-lyases0.00000003183Highly InformativeDirect
Enzyme Commission (EC)Protein-N(pi)-phosphohistidine--D-fructose phosphotransferase0.000001534Highly InformativeDirect
Enzyme Commission (EC)Acyl groups converted into alkyl groups on transfer0.2265Highly InformativeInherited
Enzyme Commission (EC)Aldehyde-lyases0.2744Highly InformativeInherited
Enzyme Commission (EC)Phosphotransferases (phosphomutases)1Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) ]

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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · Internal database links ]