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 (3,190) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 42,290 103,815 37
Proteins 38,230 93,766 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) nitrogen compound metabolic process 0.001566 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.1024 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
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) cellular aromatic compound metabolic 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) carbohydrate metabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 4.225e-11 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 2.715e-09 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.0001234 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.000724 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.7216 Moderately Informative Inherited
Biological Process (BP) organic hydroxy compound metabolic process 0.05345 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.7917 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound biosynthetic process 0.3138 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3466 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.04174 Moderately Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) single-organism biosynthetic process 0.02601 Moderately Informative Inherited
Biological Process (BP) pyridine-containing compound metabolic process 0 Informative Direct
Biological Process (BP) carbohydrate catabolic process 6.134e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 7.113e-07 Informative Direct
Biological Process (BP) lipid catabolic process 1.56e-06 Informative Direct
Biological Process (BP) carbohydrate biosynthetic process 2.461e-05 Informative Direct
Biological Process (BP) cellular carbohydrate metabolic process 5.093e-05 Informative Direct
Biological Process (BP) polysaccharide metabolic process 0.0004644 Informative Direct
Biological Process (BP) alcohol metabolic process 0.916 Informative Inherited
Biological Process (BP) coenzyme biosynthetic process 1 Informative Inherited
Biological Process (BP) cellular amide metabolic process 0.05324 Informative Inherited
Biological Process (BP) vitamin metabolic process 0.5611 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) nucleotide biosynthetic process 1 Informative Inherited
Biological Process (BP) fatty acid metabolic process 0.001895 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.7452 Informative Inherited
Biological Process (BP) hexose metabolic process 0.8513 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.107 Informative Inherited
Biological Process (BP) nicotinamide nucleotide metabolic process 0 Highly Informative Direct
Biological Process (BP) polyol metabolic process 1.944e-08 Highly Informative Direct
Biological Process (BP) branched-chain amino acid metabolic process 3.558e-08 Highly Informative Direct
Biological Process (BP) lipid modification 1.273e-07 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 1.699e-07 Highly Informative Direct
Biological Process (BP) response to osmotic stress 1.143e-05 Highly Informative Direct
Biological Process (BP) amide biosynthetic process 0.0008457 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.0008882 Highly Informative Direct
Biological Process (BP) nucleotide-sugar metabolic process 0.004457 Highly Informative Inherited
Biological Process (BP) cellular modified amino acid biosynthetic process 0.1368 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.2268 Moderately Informative Inherited
Molecular Function (MF) isomerase activity 0.08898 Moderately Informative Inherited
Molecular Function (MF) lyase activity 0.07597 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) hydro-lyase activity 1.687e-10 Informative Direct
Molecular Function (MF) nucleotide binding 2.121e-10 Informative Direct
Molecular Function (MF) racemase and epimerase activity 3.417e-05 Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity 0.0303 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 3.054e-15 Highly Informative Direct
Molecular Function (MF) intramolecular oxidoreductase activity, transposing C=C bonds 1.741e-08 Highly Informative Direct
Molecular Function (MF) NADP binding 3.348e-05 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 0.003854 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1459 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytosol 8.942e-05 Moderately Informative Direct
Cellular Component (CC) microbody 7.99e-13 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)Isomerases1.634e-11Least 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 oxidoreductases1.304e-11Moderately 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 homeostasis0.6998Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.01448Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal fatty acid level0.0002065Highly 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)fertile0Least 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)Lyases0.1804Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases9.772e-11Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases2.119e-11InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0007377InformativeDirect
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 donor0.01887Highly 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 processMethanogenesis1.907e-09Highly InformativeDirect
Biological processLipid degradation3.183e-08Highly InformativeDirect
Biological processAromatic amino acid biosynthesis1Highly InformativeInherited
Cellular componentCytoplasm2.213e-07Least InformativeDirect
Cellular componentPeroxisome4.39e-06InformativeDirect
DiseaseCrown gall tumor7.708e-07InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Molecular functionNADP0InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationLyase4.093e-10Moderately InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)lipid metabolism0Least InformativeDirect
UniPathway (UP)amino-acid metabolism1Least InformativeInherited
UniPathway (UP)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)membrane lipid metabolism0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation0.749Moderately InformativeInherited
UniPathway (UP)carbohydrate degradation0.8124Moderately InformativeInherited
UniPathway (UP)fatty acid metabolism1Moderately InformativeInherited
UniPathway (UP)glycan metabolism1Moderately InformativeInherited
UniPathway (UP)pentose phosphate pathway0InformativeDirect
UniPathway (UP)lipid degradation0InformativeDirect
UniPathway (UP)glycerophospholipid metabolism0InformativeDirect
UniPathway (UP)Branched-chain amino-acid degradation2.112e-15InformativeDirect
UniPathway (UP)alginate metabolism7.233e-06InformativeDirect
UniPathway (UP)phospholipid metabolism1InformativeInherited
UniPathway (UP)L-valine degradation0Highly InformativeDirect
UniPathway (UP)alpha-glycerophosphate cycle1.076e-10Highly InformativeDirect
UniPathway (UP)D-arabinitol metabolism1.153e-05Highly 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 ]