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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 2018_03 genome PDB chains (SCOP 1.75)
Domains 43,349 342,022 37
Proteins 39,167 309,868 36


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)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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.02964Least InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.00002186InformativeDirect

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) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect

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 tissue0.000514Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0.6306Least 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 stage0.0002938Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0.0003026Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0.0003722Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0.000636Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0.000689Least 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)Lyases0.3411Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0.00000000001486Moderately InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0InformativeDirect
Enzyme Commission (EC)Intramolecular oxidoreductases0.000000000006905InformativeDirect
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0.0003998InformativeDirect
Enzyme Commission (EC)Acting on the aldehyde or oxo group of donors1InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH group of donors1InformativeInherited
Enzyme Commission (EC)Intramolecular transferases1InformativeInherited
Enzyme Commission (EC)Transposing C=C bonds0Highly InformativeDirect
Enzyme Commission (EC)Acting on hydrogen as donors0.01611Highly InformativeInherited
Enzyme Commission (EC)With an iron-sulfur protein as acceptor0.03577Highly InformativeInherited

Document: EC 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 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 · Enzyme Commission (EC) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]