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  Home > SCOP hierarchy > PLP-dependent transferases superfamily


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 (3,262) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 107,854 815,881 166
Proteins 105,575 801,712 166

 Functional annotation
General category Metabolism
Detailed category Transferases

Document: Function annotation of SCOP domain superfamilies

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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.219Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating metabolite concentration0.007261Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of serum amino acid level0.00000884InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal homeostasis0.006067Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.5056Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.699Least InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.3166Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.4818Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal amino acid level0.0001799InformativeDirect
Mammalian Phenotype (MP)abnormal systemic arterial blood pressure0.01919InformativeInherited
Mammalian Phenotype (MP)hypertension0.0003915Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism environmental stimulus response variant0.1165Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.2924Least InformativeInherited
Worm Phenotype (WP)cell physiology variant0.3697Least InformativeInherited
Worm Phenotype (WP)movement variant0.3188Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant0.4248Moderately InformativeInherited
Worm Phenotype (WP)apoptosis variant0.4984Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.6431Moderately InformativeInherited
Worm Phenotype (WP)organism ionizing radiation response variant0.01724InformativeInherited
Worm Phenotype (WP)forward locomotion variant0.02018InformativeInherited
Worm Phenotype (WP)cell stress response variant0.02818InformativeInherited
Worm Phenotype (WP)body posture variant0.04761InformativeInherited
Worm Phenotype (WP)defecation variant0.05547InformativeInherited
Worm Phenotype (WP)mutagen induced apoptosis variant0.0001017Highly InformativeDirect
Worm Phenotype (WP)defecation contraction variant0.0001314Highly InformativeDirect
Worm Phenotype (WP)germ cell ionizing radiation response variant0.005863Highly InformativeInherited
Worm Phenotype (WP)body posture amplitude variant0.01347Highly InformativeInherited
Worm Phenotype (WP)path curvature variant0.05723Highly InformativeInherited

Document: WP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)trunk0.2037Least InformativeInherited
Xenopus ANatomical entity (XAN)cavitated compound organ0.3783Least InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.00223Moderately InformativeInherited
Xenopus ANatomical entity (XAN)viscus0.007435Moderately InformativeInherited
Xenopus ANatomical entity (XAN)intestine0.00006025InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases1Least InformativeInherited
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Transferring groups other than amino-acyl groups0Moderately InformativeDirect
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)Carbon-carbon lyases0.0000000000001165Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups0.00000002587Moderately InformativeDirect
Enzyme Commission (EC)Carbon-oxygen lyases1Moderately InformativeInherited
Enzyme Commission (EC)Ligases1Moderately InformativeInherited
Enzyme Commission (EC)Acting on the CH-NH(2) group of donors0InformativeDirect
Enzyme Commission (EC)Hydroxymethyl-, formyl- and related transferases0InformativeDirect
Enzyme Commission (EC)Transferring sulfur-containing groups0InformativeDirect
Enzyme Commission (EC)Intramolecular transferases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.7009InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Transferring nitrogenous groups0Highly InformativeDirect
Enzyme Commission (EC)Sulfurtransferases0Highly InformativeDirect
Enzyme Commission (EC)Other carbon-carbon lyases0.000000006757Highly InformativeDirect
Enzyme Commission (EC)Aldehyde-lyases0.8391Highly InformativeInherited
Enzyme Commission (EC)In ketonic substances1Highly InformativeInherited
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited
Enzyme Commission (EC)Acid--thiol ligases1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Post-translational modificationOxidoreductase0Moderately InformativeDirect

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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 259 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 259 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2013 The SUPERFAMILY authors and Julian Gough.