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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 (2,868) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,995 45,513 56
Proteins 7,976 45,503 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 0.00000002211 Least Informative Direct
Biological Process (BP) cellular nitrogen compound 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) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.8576 Least Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000000000000028 Moderately Informative Direct
Biological Process (BP) nucleoside phosphate metabolic process 0.0000000008229 Moderately Informative Direct
Biological Process (BP) purine-containing compound metabolic process 0.00002127 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0.00007572 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002927 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0.3803 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.473 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.772 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.3153 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.8459 Moderately Informative Inherited
Biological Process (BP) nicotinamide nucleotide metabolic process 0.000000000000001945 Informative Direct
Biological Process (BP) ATP metabolic process 0.00000007122 Informative Direct
Biological Process (BP) carbohydrate catabolic process 0.0000006348 Informative Direct
Biological Process (BP) cellular respiration 0.0002647 Informative Direct
Biological Process (BP) phosphorylation 0.8811 Informative Inherited
Biological Process (BP) nucleoside diphosphate metabolic process 0.00424 Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0.01572 Informative Inherited
Biological Process (BP) aerobic respiration 0 Highly Informative Direct
Biological Process (BP) citrate metabolic process 0 Highly Informative Direct
Biological Process (BP) lactate metabolic process 0.00000000002384 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 0.018 Moderately Informative Inherited
Molecular Function (MF) coenzyme binding 0.0000006565 Informative Direct
Molecular Function (MF) hydrolase activity, acting on glycosyl bonds 0.00006165 Informative Direct
Molecular Function (MF) identical protein binding 0.0001833 Informative Direct
Molecular Function (MF) NAD binding 0.0000000004558 Highly Informative Direct
Molecular Function (MF) hydrolase activity, hydrolyzing O-glycosyl compounds 0.00001947 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 0.0000001196 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.9335 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.1912 Least Informative Inherited
Cellular Component (CC) mitochondrial part 0.000000126 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.02313 Moderately Informative Inherited
Cellular Component (CC) vesicle 0.4109 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.08596 Moderately Informative Inherited
Cellular Component (CC) microbody 0.0005797 Informative Direct
Cellular Component (CC) extracellular organelle 0.002456 Informative Inherited
Cellular Component (CC) extracellular vesicle 0.0002952 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)anatomical cluster0Least InformativeDirect
Xenopus ANatomical entity (XAN)tissue0.3302Least InformativeInherited
Xenopus ANatomical entity (XAN)brain0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)alimentary system0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)female genitalia0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)musculoskeletal system0.01466Moderately InformativeInherited
Xenopus ANatomical entity (XAN)tail0InformativeDirect
Xenopus ANatomical entity (XAN)duct0InformativeDirect
Xenopus ANatomical entity (XAN)skeletal muscle0.0008199InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)portion of meristem tissue0Least 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)inflorescence meristem0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)seed development stage0.00001714InformativeDirect

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)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Acting on the CH-OH group of donors0Moderately InformativeDirect
Enzyme Commission (EC)Glycosylases0.1678Moderately InformativeInherited
Enzyme Commission (EC)With NAD(+) or NADP(+) as acceptor0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTricarboxylic acid cycle0InformativeDirect
Cellular componentPeroxisome0.00002099InformativeDirect
DomainTransit peptide0.0000008393Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationOxidoreductase0Moderately InformativeDirect
Post-translational modificationGlycosidase0.000008575InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)carbohydrate metabolism0Least InformativeDirect
UniPathway (UP)organic acid metabolism0Moderately InformativeDirect
UniPathway (UP)metabolic intermediate degradation0InformativeDirect
UniPathway (UP)fermentation0InformativeDirect
UniPathway (UP)organic acid degradation0InformativeDirect
UniPathway (UP)pyruvate metabolism0Highly InformativeDirect

Document: UP 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · 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 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) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]