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PLP-dependent transferases superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   PLP-dependent transferase-like [ 53382] (3)
Superfamily:   PLP-dependent transferases [ 53383] (9)
Families:   AAT-like [ 53384] (16)
  Beta-eliminating lyases [ 53397] (2)
  Pyridoxal-dependent decarboxylase [ 69565] (3)
  Cystathionine synthase-like [ 53402] (16)
  GABA-aminotransferase-like [ 53417] (16)
  Ornithine decarboxylase major domain [ 53444]
  Glycine dehydrogenase subunits (GDC-P) [ 142678] (2)
  SelA-like [ 142683]
  SepSecS-like [ 159704]


Superfamily statistics
Genomes (3,260) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 107,539 613,650 166
Proteins 105,270 602,892 166


Functional annotation
General category Metabolism
Detailed category Transferases

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)single-organism cellular process00Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process00Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis11Least InformativeInherited
Biological Process (BP)primary metabolic process0.20151Least InformativeInherited
Biological Process (BP)macromolecule metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)small molecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process00Moderately InformativeDirect
Biological Process (BP)cellular protein modification process11Moderately InformativeInherited
Biological Process (BP)cellular component assembly0.30171Moderately InformativeInherited
Biological Process (BP)single-organism catabolic process0.062980.00000132Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.16890.0001577Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.037460.0001635Moderately InformativeInherited
Biological Process (BP)cofactor metabolic process0.015410Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)amide biosynthetic process0.00092950.1005Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.095270.03656Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.16430.03518Moderately InformativeInherited
Biological Process (BP)carbohydrate metabolic process11Moderately InformativeInherited
Biological Process (BP)dicarboxylic acid metabolic process00InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.000000000000006150InformativeDirect
Biological Process (BP)aspartate family amino acid metabolic process0.000000000032370.0000001137InformativeDirect
Biological Process (BP)cellular modified amino acid metabolic process0.014540.02545InformativeInherited
Biological Process (BP)organic hydroxy compound biosynthetic process0.018510.0007129InformativeInherited
Biological Process (BP)cellular metabolic compound salvage0.47830.03432InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.53981InformativeInherited
Biological Process (BP)cellular aldehyde metabolic process0.24850.02032InformativeInherited
Biological Process (BP)carboxylic acid catabolic process0.61140.0153InformativeInherited
Biological Process (BP)water-soluble vitamin biosynthetic process0.0019540.00005169InformativeInherited
Biological Process (BP)monocarboxylic acid biosynthetic process0.88240.4878InformativeInherited
Biological Process (BP)glutamine family amino acid metabolic process0.0000057310.01306InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.030661InformativeInherited
Biological Process (BP)carbohydrate biosynthetic process0.27860.5984InformativeInherited
Biological Process (BP)alcohol metabolic process11InformativeInherited
Biological Process (BP)cellular carbohydrate metabolic process0.53461InformativeInherited
Biological Process (BP)biotin metabolic process00Highly InformativeDirect
Biological Process (BP)glutamate metabolic process0.000000000035810.00000000000003101Highly InformativeDirect
Biological Process (BP)dicarboxylic acid biosynthetic process0.0000027080.0001402Highly InformativeDirect
Biological Process (BP)folic acid-containing compound metabolic process0.62120.5154Highly InformativeInherited
Biological Process (BP)polyol metabolic process0.00000013080.1168Highly InformativeInherited
Biological Process (BP)L-methionine salvage11Highly InformativeInherited
Biological Process (BP)peptidyl-lysine modification0.097840.6865Highly InformativeInherited
Biological Process (BP)glyoxylate metabolic process0.0021820.0001674Highly InformativeInherited
Biological Process (BP)aldehyde catabolic process0.031370.00452Highly InformativeInherited
Biological Process (BP)alcohol biosynthetic process0.1640.2785Highly InformativeInherited
Molecular Function (MF)transferase activity00Least InformativeDirect
Molecular Function (MF)binding11Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)small molecule binding00Moderately InformativeDirect
Molecular Function (MF)anion binding00.000000000000003188Moderately InformativeDirect
Molecular Function (MF)isomerase activity11Moderately InformativeInherited
Molecular Function (MF)oxidoreductase activity11Moderately InformativeInherited
Molecular Function (MF)identical protein binding0.00028680.00005046InformativeDirect
Molecular Function (MF)transferase activity, transferring sulfur-containing groups0.94480.1213InformativeInherited
Molecular Function (MF)transferase activity, transferring one-carbon groups10.4165InformativeInherited
Molecular Function (MF)carboxylic acid binding0.83710.0783InformativeInherited
Molecular Function (MF)transferase activity, transferring acyl groups10.002103InformativeInherited
Molecular Function (MF)carbon-carbon lyase activity0.74140.0000001433InformativeInherited
Molecular Function (MF)transferase activity, transferring alkyl or aryl (other than methyl) groups11InformativeInherited
Molecular Function (MF)transferase activity, transferring nitrogenous groups00Highly InformativeDirect
Molecular Function (MF)vitamin binding00Highly InformativeDirect
Molecular Function (MF)hydroxymethyl-, formyl- and related transferase activity00Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity00Highly InformativeDirect
Molecular Function (MF)sulfurtransferase activity0.00000015840.00000000000009895Highly InformativeDirect
Molecular Function (MF)amino acid binding0.0000028410.000000005573Highly InformativeDirect
Molecular Function (MF)oxidoreductase activity, acting on the CH-NH2 group of donors0.000016890.000000000281Highly InformativeDirect
Molecular Function (MF)intramolecular transferase activity0.007480.026Highly InformativeInherited
Molecular Function (MF)acetyltransferase activity0.033851Highly InformativeInherited
Molecular Function (MF)aldehyde-lyase activity0.024680.2178Highly InformativeInherited
Molecular Function (MF)carboxy-lyase activity0.15130.000196Highly InformativeInherited
Cellular Component (CC)cytoplasmic part0.00099460.0000000002056Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.36130.9326Least InformativeInherited
Cellular Component (CC)intracellular organelle part11Least InformativeInherited
Cellular Component (CC)intracellular organelle lumen0.98381Moderately InformativeInherited
Cellular Component (CC)microbody0.000047060.00004303InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) biological regulation 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) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) small molecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) cofactor metabolic process 0 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.0001635 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.00000132 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.0001577 Moderately Informative Direct
Biological Process (BP) protein complex biogenesis 0.6407 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.03656 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) amide biosynthetic process 0.1005 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.03518 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) dicarboxylic acid metabolic process 0 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) aspartate family amino acid metabolic process 0.0000001137 Informative Direct
Biological Process (BP) water-soluble vitamin biosynthetic process 0.00005169 Informative Direct
Biological Process (BP) organic hydroxy compound biosynthetic process 0.0007129 Informative Direct
Biological Process (BP) tetrapyrrole metabolic process 0.0000003866 Informative Direct
Biological Process (BP) ammonium ion metabolic process 0.0000948 Informative Direct
Biological Process (BP) membrane lipid metabolic process 0 Informative Direct
Biological Process (BP) protein oligomerization 0.01347 Informative Inherited
Biological Process (BP) response to nitrogen compound 1 Informative Inherited
Biological Process (BP) behavior 0.8162 Informative Inherited
Biological Process (BP) cellular modified amino acid metabolic process 0.02545 Informative Inherited
Biological Process (BP) cellular aldehyde metabolic process 0.02032 Informative Inherited
Biological Process (BP) pigment metabolic process 0.238 Informative Inherited
Biological Process (BP) amine metabolic process 0.003928 Informative Inherited
Biological Process (BP) response to organic cyclic compound 0.7113 Informative Inherited
Biological Process (BP) cellular metabolic compound salvage 0.03432 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 1 Informative Inherited
Biological Process (BP) monocarboxylic acid biosynthetic process 0.4878 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 0.0153 Informative Inherited
Biological Process (BP) glutamine family amino acid metabolic process 0.01306 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 1 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.5984 Informative Inherited
Biological Process (BP) alcohol metabolic process 1 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 1 Informative Inherited
Biological Process (BP) biotin metabolic process 0 Highly Informative Direct
Biological Process (BP) glutamate metabolic process 0.00000000000003101 Highly Informative Direct
Biological Process (BP) dicarboxylic acid biosynthetic process 0.0001402 Highly Informative Direct
Biological Process (BP) serine family amino acid metabolic process 0.000000004094 Highly Informative Direct
Biological Process (BP) glyoxylate metabolic process 0.0001674 Highly Informative Direct
Biological Process (BP) imidazole-containing compound metabolic process 0.0000009543 Highly Informative Direct
Biological Process (BP) protein homotetramerization 0.0002536 Highly Informative Direct
Biological Process (BP) benzene-containing compound metabolic process 0.00002446 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0.000961 Highly Informative Direct
Biological Process (BP) heme biosynthetic process 0.0002811 Highly Informative Direct
Biological Process (BP) sphingolipid biosynthetic process 0.000739 Highly Informative Direct
Biological Process (BP) single-organism behavior 0.7073 Highly Informative Inherited
Biological Process (BP) folic acid-containing compound metabolic process 0.5154 Highly Informative Inherited
Biological Process (BP) polyol metabolic process 0.1168 Highly Informative Inherited
Biological Process (BP) L-methionine salvage 1 Highly Informative Inherited
Biological Process (BP) peptidyl-lysine modification 0.6865 Highly Informative Inherited
Biological Process (BP) aldehyde catabolic process 0.00452 Highly Informative Inherited
Biological Process (BP) alcohol biosynthetic process 0.2785 Highly Informative Inherited
Molecular Function (MF) transferase activity 0 Least Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000000000000003188 Moderately Informative Direct
Molecular Function (MF) isomerase activity 1 Moderately Informative Inherited
Molecular Function (MF) oxidoreductase activity 1 Moderately Informative Inherited
Molecular Function (MF) identical protein binding 0.00005046 Informative Direct
Molecular Function (MF) carbon-carbon lyase activity 0.0000001433 Informative Direct
Molecular Function (MF) transferase activity, transferring sulfur-containing groups 0.1213 Informative Inherited
Molecular Function (MF) transferase activity, transferring one-carbon groups 0.4165 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.0783 Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.002103 Informative Inherited
Molecular Function (MF) transferase activity, transferring alkyl or aryl (other than methyl) groups 1 Informative Inherited
Molecular Function (MF) transferase activity, transferring nitrogenous groups 0 Highly Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Molecular Function (MF) hydroxymethyl-, formyl- and related transferase activity 0 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0 Highly Informative Direct
Molecular Function (MF) sulfurtransferase activity 0.00000000000009895 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.000000005573 Highly Informative Direct
Molecular Function (MF) oxidoreductase activity, acting on the CH-NH2 group of donors 0.000000000281 Highly Informative Direct
Molecular Function (MF) carboxy-lyase activity 0.000196 Highly Informative Direct
Molecular Function (MF) intramolecular transferase activity 0.026 Highly Informative Inherited
Molecular Function (MF) acetyltransferase activity 1 Highly Informative Inherited
Molecular Function (MF) aldehyde-lyase activity 0.2178 Highly Informative Inherited
Cellular Component (CC) cytoplasmic part 0.0000000002056 Least Informative Direct
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.9326 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) organelle inner membrane 0.00007689 Moderately Informative Direct
Cellular Component (CC) transferase complex 0.6201 Moderately Informative Inherited
Cellular Component (CC) endomembrane system 1 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 1 Moderately Informative Inherited
Cellular Component (CC) mitochondrial envelope 1 Moderately Informative Inherited
Cellular Component (CC) microbody 0.00004303 Informative Direct
Cellular Component (CC) endoplasmic reticulum membrane 0.08895 Informative Inherited
Cellular Component (CC) oxidoreductase complex 0.07539 Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.00000002923Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Carboxy-lyases1Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Sulfurtransferases0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Transferring nitrogenous groups0InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.821InformativeInherited
Enzyme Commission (EC)Glutamate decarboxylase0Highly InformativeDirect
Enzyme Commission (EC)Molybdenum cofactor sulfurtransferase0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0Highly InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly 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 metabolism1Moderately InformativeInherited
Biological processAntibiotic resistance0.000000000006232InformativeDirect
Biological processLipid biosynthesis1InformativeInherited
Biological processPyridine nucleotide biosynthesis0Highly InformativeDirect
Biological processHistidine biosynthesis0Highly InformativeDirect
Biological processOne-carbon metabolism0Highly InformativeDirect
Biological processPorphyrin biosynthesis0Highly InformativeDirect
Biological processSphingolipid metabolism0Highly InformativeDirect
Biological processChlorophyll biosynthesis0Highly InformativeDirect
Biological processLipopolysaccharide biosynthesis0.00000000000000286Highly InformativeDirect
Biological processHeme biosynthesis0.00000000000003279Highly InformativeDirect
Biological processAntibiotic biosynthesis0.00000000000006282Highly InformativeDirect
Biological processMolybdenum cofactor biosynthesis0.0000000000327Highly InformativeDirect
Biological processArginine metabolism0.000000001327Highly InformativeDirect
Biological processLipid A biosynthesis0.00005619Highly InformativeDirect
Biological processPhenylalanine catabolism0.0009319Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DomainTransit peptide0Moderately InformativeDirect
Molecular functionMetal-binding1Least InformativeInherited
Molecular functionIron-sulfur0.0001475Moderately InformativeDirect
Molecular function2Fe-2S0InformativeDirect
Molecular functionSelenium0Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Molecular functionPyruvate0.00000000446Highly InformativeDirect
Post-translational modificationTransferase0Least InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationLyase0.00000008485Moderately InformativeDirect
Post-translational modificationDecarboxylase0Highly InformativeDirect
Post-translational modificationNitration0.000001412InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR015424 SSF53383 Protein matches
Abstract

This entry represents the major region of PLP-dependent transferases. This domain has a three layer alpha/beta/alpha sandwich topology, with mixed beta-sheets of 7 strands. The major region can be found in the following PLP-dependent transferase families:

  • Aspartate aminotransferase (AAT)-like enzymes, such as aromatic aminoacid aminotransferase AroAT, glutamine aminotransferase and kynureninase [PubMed17300176].
  • Beta-eliminating lyases, such as tyrosine phenol lyase and tryptophanase [PubMed16790938].
  • Pyridoxal-dependent decarboxylases, such as DOPA decarboxylase and glutamate decarboxylase beta (GadB) [PubMed15690345].
  • Cystathionine synthase-like enzymes, such as cystalysin, methionine gamma-lyase (MGL), and cysteine desulphurase (IscS) [PubMed17014820].
  • GABA-aminotransferase-like enzymes, such as ornithine aminotransferase and serine hydroxymethyltransferase [PubMed15848278].
  • Ornithine decarboxylase major domain [PubMed10666573].

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-quality) · 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 92 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 PLP-dependent transferases 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 92 hidden Markov models representing the PLP-dependent transferases 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]