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6-phosphogluconate dehydrogenase C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   6-phosphogluconate dehydrogenase C-terminal domain-like [ 48178]
Superfamily:   6-phosphogluconate dehydrogenase C-terminal domain-like [ 48179] (12)
Families:   Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain [ 48180] (2)
  Mannitol 2-dehydrogenase [ 81843]
  Acetohydroxy acid isomeroreductase (ketol-acid reductoisomerase, KARI) [ 48184] (2)
  HCDH C-domain-like [ 48187] (2)
  Conserved hypothetical protein MTH1747 [ 74762]
  UDP-glucose/GDP-mannose dehydrogenase dimerisation domain [ 48191] (2)
  N-(1-D-carboxylethyl)-L-norvaline dehydrogenase [ 48194]
  Glycerol-3-phosphate dehydrogenase [ 48197]
  Ketopantoate reductase PanE [ 69084]
  ProC C-terminal domain-like [ 116984] (2)
  HMD dimerization domain-like [ 140777]
  TyrA dimerization domain-like [ 140780]


Superfamily statistics
Genomes (3,240) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 43,349 255,626 37
Proteins 39,167 232,149 36


Functional annotation
General category Metabolism
Detailed category Energy

Document:
Function annotation of SCOP domain superfamilies

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) single-organism cellular process 0.000000000000009084 Least Informative Direct
Biological Process (BP) primary metabolic process 0.01917 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.009072 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.7817 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 0.5529 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 0.6446 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.000000009051 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.0001287 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.000000005868 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0003926 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00000000000004736 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.00000000000006667 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00699 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.9332 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7063 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.2135 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.4786 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.5865 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.004487 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.1526 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.09025 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.00701 Moderately Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.000000002623 Informative Direct
Biological Process (BP) cellular aldehyde metabolic process 0 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.000885 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.0000003268 Informative Direct
Biological Process (BP) response to oxidative stress 0.0001191 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 0.00003844 Informative Direct
Biological Process (BP) lipid catabolic process 0.0000000000344 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.000002542 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.0006327 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.000008766 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0001051 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) alpha-amino acid biosynthetic process 0.0006017 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 0.163 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 1 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 1 Informative Inherited
Biological Process (BP) alcohol metabolic process 0.9292 Informative Inherited
Biological Process (BP) NADP metabolic process 0.00000000004962 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.00001674 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.00000000005487 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.00002071 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000003316 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.0007317 Highly Informative Direct
Biological Process (BP) glyceraldehyde-3-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) lipid modification 0.00001426 Highly Informative Direct
Biological Process (BP) cellular polysaccharide biosynthetic process 0.000006115 Highly Informative Direct
Biological Process (BP) glucose 6-phosphate metabolic process 0 Highly Informative Direct
Biological Process (BP) polyol metabolic process 0.003148 Highly Informative Inherited
Biological Process (BP) cellular modified amino acid biosynthetic process 0.005657 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.03206 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.000000345 Moderately Informative Direct
Molecular Function (MF) anion binding 0.3178 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.003842 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.002795 Moderately Informative Inherited
Molecular Function (MF) hydro-lyase activity 0 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.0000001139 Informative Direct
Molecular Function (MF) coenzyme binding 0 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.09009 Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.000001394 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors 0.0001031 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0.00000000004905 Highly Informative Direct
Molecular Function (MF) NADP binding 0.0001965 Highly Informative Direct
Molecular Function (MF) NAD binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 0.9639 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0009739 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) microbody 0.0000000002017 Informative Direct
Cellular Component (CC) chromosome 0.7603 Informative Inherited
Cellular Component (CC) protein-DNA complex 0.01368 Informative Inherited
Cellular Component (CC) chromatin 0.2605 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000001634Least InformativeDirect
Enzyme Commission (EC)Lyases0.04828Least InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0Moderately InformativeDirect
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.00000000001304Moderately InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-CH group of donors1Moderately InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)3-hydroxybutyryl-CoA epimerase0Highly InformativeDirect
Enzyme Commission (EC)3-hydroxyacyl-CoA dehydrogenase0Highly InformativeDirect
Enzyme Commission (EC)Dodecenoyl-CoA isomerase0Highly InformativeDirect
Enzyme Commission (EC)Enoyl-CoA hydratase0Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.003492Highly 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 processLipid metabolism0Moderately InformativeDirect
Biological processLipid degradation0.0000001847InformativeDirect
Biological processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Biological processMethanogenesis0.000000001833Highly InformativeDirect
Biological processAromatic amino acid biosynthesis1Highly InformativeInherited
Cellular componentCytoplasm0.0000002415Least InformativeDirect
Cellular componentPeroxisome0.000006746InformativeDirect
DiseaseCrown gall tumor0.0000008522InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNADP0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.0000000002379Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008927 SSF48179 Protein matches
Abstract

6-phosphogluconate dehydrogenase catalyses the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate with the concomitant reduction of NADP to NADPH. The metazoan 6PGDHs have a well-conserved glycine-serine rich sequence at the C-terminus, which is lacking from bacterial enzymes and from those of the parasitic protozoan Trypanosoma brucei. The active dimer of the mammalian enzyme assembles with the C-terminal tail of one subunit threaded through the other, forming part of the substrate-binding site. The tail of T. brucei 6PGDH is shorter than that of the mammalian enzyme and its terminal residues associate tightly with the second monomer. The three-dimensional structure shows this generates additional interactions between the subunits close to the active site; the coenzyme-binding domain is thereby associated more tightly with the helical domain. Three residues, conserved in all other known sequences, are important in creating a salt bridge between monomers close to the substrate-binding site [PubMed9737929].

This domain is structurally similar to domains found in several different families, including those represented by mannitol 2-dehydrogenase, acetohydroxy acid isomeroreductase, short chain L-3-hydroxyacyl CoA dehydrogenase, UDP-glucose/GDP-mannose dehydrogenase (dimerisation domain), N-(1-D-carboxylethyl)-L-norvaline dehydrogenase, glycerol-3-phosphate dehydrogenase, and ketopantoate reductase (PanE).


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-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 26 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 6-phosphogluconate dehydrogenase C-terminal domain-like 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 26 hidden Markov models representing the 6-phosphogluconate dehydrogenase C-terminal domain-like 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]