SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,232) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 43,152 242,182 37
Proteins 38,988 217,639 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) response to stimulus 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.02027 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.08767 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 0.002317 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.00000000000001752 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000000000362 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0.00000000002276 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.00000000004635 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0.0000000003078 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.7812 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.02212 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.1081 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.2286 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0.2049 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4151 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.01335 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.7771 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.000000007495 Informative Direct
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.0000001297 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0000002325 Informative Direct
Biological Process (BP) lipid catabolic process 0.0000004425 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 0.00008025 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 0.00009465 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.0004784 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0007183 Informative Direct
Biological Process (BP) alcohol metabolic process 0.9265 Informative Inherited
Biological Process (BP) hexose metabolic process 0.6587 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) amide biosynthetic process 0.001073 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 1 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.563 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.5734 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 1 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.1221 Informative Inherited
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0 Highly Informative Direct
Biological Process (BP) alditol metabolic process 0.0000000004278 Highly Informative Direct
Biological Process (BP) monosaccharide catabolic process 0.0000000006503 Highly Informative Direct
Biological Process (BP) lipid modification 0.00000003005 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.00000003589 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 0.0000000803 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.0009887 Highly Informative Direct
Biological Process (BP) cellular modified amino acid biosynthetic process 0.1622 Highly Informative Inherited
Biological Process (BP) nucleotide-sugar metabolic process 0.005484 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 0.00000008506 Moderately Informative Direct
Molecular Function (MF) anion binding 0.2764 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.1391 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.1224 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on CH-OH group of donors 0 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.0000000005559 Informative Direct
Molecular Function (MF) hydro-lyase activity 0.000000001093 Informative Direct
Molecular Function (MF) racemase and epimerase activity 0.00006565 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.02853 Informative Inherited
Molecular Function (MF) NAD binding 0 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor 0 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 0.00000002024 Highly Informative Direct
Molecular Function (MF) NADP binding 0.00004738 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-CH group of donors 1 Highly Informative Inherited
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 0.002218 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.01743 Least Informative Inherited
Cellular Component (CC) cytosol 0.0003913 Moderately Informative Direct
Cellular Component (CC) microbody 0.0000000000009566 Informative Direct

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

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.6574Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.01471Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fatty acid level0.0002058Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)viable0Least InformativeDirect
Fly Phenotype (FP)fertile0Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0Least InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0.0005109Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0.6297Least InformativeInherited
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 stage0.0002929Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0003016Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0003721Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0.0006338Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0.0006887Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Lyases0.185Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000004672Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.00000000001695InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0007076InformativeDirect
Enzyme Commission (EC)Acting on the CH-NH group of donors1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases (mutases)1InformativeInherited
Enzyme Commission (EC)Transposing C==C bonds0Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donor0.01812Highly 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 processBranched-chain amino acid biosynthesis0Highly InformativeDirect
Biological processPhospholipid metabolism0Highly InformativeDirect
Biological processMethanogenesis0.000000001795Highly InformativeDirect
Biological processLipid degradation0.00000003391Highly InformativeDirect
Biological processAromatic amino acid biosynthesis1Highly InformativeInherited
Cellular componentCytoplasm0.0000004828Least InformativeDirect
Cellular componentPeroxisome0.000004035InformativeDirect
DiseaseCrown gall tumor0.0000007863InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase0.0000000008666Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)biopolymer metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)aromatic compound metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)fatty acid metabolism0.1855Moderately InformativeInherited
UniPathway (UP)organic acid metabolism0.8021Moderately InformativeInherited
UniPathway (UP)biopolymer biosynthesis1Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation1Moderately InformativeInherited
UniPathway (UP)metabolic intermediate biosynthesis1Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)glycan metabolism1Moderately InformativeInherited
UniPathway (UP)one-carbon metabolism1Moderately InformativeInherited
UniPathway (UP)amine and polyamine metabolism1Moderately InformativeInherited
UniPathway (UP)nucleotide metabolism1Moderately InformativeInherited
UniPathway (UP)aromatic compound biosynthesis1Moderately InformativeInherited
UniPathway (UP)cellular component biogenesis1Moderately InformativeInherited
UniPathway (UP)L-isoleucine biosynthesis0InformativeDirect
UniPathway (UP)fatty acid degradation0InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation0.0000000000002844InformativeDirect
UniPathway (UP)carnitine metabolism0.0000000006357InformativeDirect
UniPathway (UP)methanogenesis0.00004885InformativeDirect
UniPathway (UP)nucleotide-sugar biosynthesis0.0004644InformativeDirect
UniPathway (UP)phospholipid metabolism1InformativeInherited
UniPathway (UP)glycolipid biosynthesis1InformativeInherited
UniPathway (UP)aromatic amino-acid biosynthesis1InformativeInherited
UniPathway (UP)UDP-alpha-D-glucuronate biosynthesis0Highly InformativeDirect
UniPathway (UP)L-valine biosynthesis0Highly InformativeDirect
UniPathway (UP)L-tyrosine biosynthesis0Highly InformativeDirect
UniPathway (UP)glycerophospholipid metabolism0Highly InformativeDirect
UniPathway (UP)pentose phosphate pathway4.527e-16Highly InformativeDirect
UniPathway (UP)pentose and glucuronate interconversion0.00000000000001144Highly InformativeDirect
UniPathway (UP)methanogenesis from CO(2)0.000000005518Highly InformativeDirect
UniPathway (UP)alginate biosynthesis0.00000187Highly InformativeDirect
UniPathway (UP)enterobacterial common antigen biosynthesis0.000002955Highly InformativeDirect
UniPathway (UP)butanoate metabolism0.000179Highly InformativeDirect
UniPathway (UP)L-proline biosynthesis0.0002025Highly InformativeDirect
UniPathway (UP)prephenate biosynthesis0.0002451Highly InformativeDirect

Document: UP 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]