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LDH C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   LDH C-terminal domain-like [ 56326]
Superfamily:   LDH C-terminal domain-like [ 56327] (2)
Families:   Lactate & malate dehydrogenases, C-terminal domain [ 56328] (4)
  AglA-like glucosidase [ 90050] (4)


Superfamily statistics
Genomes (2,871) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,030 42,733 56
Proteins 8,011 42,685 56


Functional annotation
General category Metabolism
Detailed category Redox

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 0.00000002438 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.8643 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.0002719 Moderately Informative Direct
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000000006197 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00006491 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.00000000000002769 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.00001805 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.391 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.4617 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.7599 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.307 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.8348 Moderately Informative Inherited
Biological Process (BP) oxidoreduction coenzyme metabolic process 0.00000000000001079 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000006323 Informative Direct
Biological Process (BP) cellular respiration 0.0002025 Informative Direct
Biological Process (BP) ATP metabolic process 0.00000005525 Informative Direct
Biological Process (BP) pyridine-containing compound metabolic process 0.000000000000007296 Informative Direct
Biological Process (BP) phosphorylation 0.8861 Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0.01444 Informative Inherited
Biological Process (BP) lactate metabolic process 0.00000000003309 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) oxidoreductase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.01615 Moderately Informative Inherited
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.00005327 Informative Direct
Molecular Function (MF) identical protein binding 0.0002497 Informative Direct
Molecular Function (MF) coenzyme binding 0.000000627 Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing O-glycosyl compounds 0.00001692 Highly Informative Direct
Molecular Function (MF) NAD binding 0.0000000003929 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 1 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.000000081 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.931 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1917 Least Informative Inherited
Cellular Component (CC) vesicle 0.393 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.02209 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.08743 Moderately Informative Inherited
Cellular Component (CC) microbody 0.0005301 Informative Direct
Cellular Component (CC) extracellular organelle 0.001969 Informative Inherited
Cellular Component (CC) extracellular space 0.3904 Informative Inherited
Cellular Component (CC) plastid 0.02384 Informative Inherited
Cellular Component (CC) extracellular exosome 0.0009539 Highly 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)With NAD(+) or NADP(+) as acceptor0Moderately InformativeDirect
Enzyme Commission (EC)Glycosidases, i.e. enzymes hydrolyzing O- and S-gl0.09514Moderately InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTricarboxylic acid cycle0InformativeDirect
Cellular componentPeroxisome0.00002007InformativeDirect
DomainTransit peptide0.0000009236Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycosidase0.000008567InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015955 SSF56327 Protein matches
Abstract

This entry represents a structural motif found at the C-terminal of lactate dehydrogenase and malate dehydrogenases , as well as at the C-terminal of family 4 glycoside hydrolases . These domains have an unusual fold consisting of segregated alpha-helical and beta-sheet regions, although they contain predominantly anti-parallel beta-sheets [PubMed11276087, PubMed8117664, PubMed12588867].

L-lactate dehydrogenases are metabolic enzymes that catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle.

O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [PubMed7624375, PubMed8535779]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 4 comprises enzymes with several known activities; 6-phospho-beta-glucosidase ; 6-phospho-alpha-glucosidase ; alpha-galactosidase .


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 33 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 LDH 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 33 hidden Markov models representing the LDH 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 ]