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Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Tryptophan synthase beta subunit-like PLP-dependent enzymes [ 53685]
Superfamily:   Tryptophan synthase beta subunit-like PLP-dependent enzymes [ 53686]
Families:   Tryptophan synthase beta subunit-like PLP-dependent enzymes [ 53687] (8)


Superfamily statistics
Genomes (3,057) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,857 117,865 39
Proteins 21,743 117,766 39


Functional annotation
General category Metabolism
Detailed category Amino acids metabolism and transport

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)biosynthetic process0.0000033850.0000000114Least InformativeDirect
Biological Process (BP)primary metabolic process0.000039630.0001056Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000000012720Least InformativeDirect
Biological Process (BP)organonitrogen compound metabolic process0.00000000000064720Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process00Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.0000000032440.00000000000009312Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process11Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process11Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process11Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.39580.386Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.000000000010740.000000000000001945InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.000000000004290InformativeDirect
Biological Process (BP)amine metabolic process0.32080.004397InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.000041820.005861InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process10.08261InformativeInherited
Biological Process (BP)serine family amino acid metabolic process00Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process0.0000057310.000000000006025Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.0026350.0000001161Highly InformativeInherited
Molecular Function (MF)binding0.22511Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.0000000000010430Moderately InformativeDirect
Molecular Function (MF)anion binding0.0000025220.000001501Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.0025720.009444Moderately InformativeInherited
Molecular Function (MF)racemase and epimerase activity0.000000000022770.00000000007886InformativeDirect
Molecular Function (MF)identical protein binding0.00032710.00005701InformativeDirect
Molecular Function (MF)protein dimerization activity0.00014160.00003856InformativeDirect
Molecular Function (MF)carboxylic acid binding0.56280.09873InformativeInherited
Molecular Function (MF)hydro-lyase activity11InformativeInherited
Molecular Function (MF)amino acid binding0.000019550.00000001946Highly InformativeDirect
Molecular Function (MF)vitamin binding00Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity0.0036360.001682Highly InformativeInherited
Molecular Function (MF)carbon-oxygen lyase activity, acting on phosphates0.3310.734Highly InformativeInherited

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) biosynthetic process 0.0000000114 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0001056 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
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) cellular amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) small molecule biosynthetic process 0.00000000000009312 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.4516 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.386 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.3605 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.000000000000001945 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) amine metabolic process 0.004397 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.005861 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.08261 Informative Inherited
Biological Process (BP) carboxylic acid catabolic process 1 Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.000004587 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000000006025 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0.0000001161 Highly Informative Direct
Molecular Function (MF) binding 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 0.000001501 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.009444 Moderately Informative Inherited
Molecular Function (MF) racemase and epimerase activity 0.00000000007886 Informative Direct
Molecular Function (MF) identical protein binding 0.00005701 Informative Direct
Molecular Function (MF) protein dimerization activity 0.00003856 Informative Direct
Molecular Function (MF) carboxylic acid binding 0.09873 Informative Inherited
Molecular Function (MF) hydro-lyase activity 1 Informative Inherited
Molecular Function (MF) amino acid binding 0.00000001946 Highly Informative Direct
Molecular Function (MF) vitamin binding 0 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0.001682 Highly Informative Inherited
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0.734 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) plastid 0.001193 Informative Inherited
Cellular Component (CC) chloroplast stroma 0.00005545 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)Lyases0Least InformativeDirect
Enzyme Commission (EC)Isomerases1Least InformativeInherited
Enzyme Commission (EC)Hydro-lyases0Moderately InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0.6368Moderately InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than meth1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Acting on amino acids and derivatives0.1365InformativeInherited
Enzyme Commission (EC)Acting on phosphates1InformativeInherited
Enzyme Commission (EC)In other compounds0Highly InformativeDirect
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.2026Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.01378Moderately InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0.4209Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.02738Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0000008117InformativeDirect

Document: YP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)seed development stage0.0003478InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Lyases0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Carbon-oxygen lyases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0.001448Moderately InformativeInherited
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0.3996InformativeInherited
Enzyme Commission (EC)Transferring alkyl or aryl groups, other than methyl groups1InformativeInherited
Enzyme Commission (EC)Ammonia-lyases0Highly InformativeDirect
Enzyme Commission (EC)Acting on amino acids and derivatives0.0275Highly InformativeInherited
Enzyme Commission (EC)Carbon-sulfur lyases1Highly 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 processAromatic amino acid biosynthesis0Highly InformativeDirect
Biological processCysteine biosynthesis0Highly InformativeDirect
Biological processGluconeogenesis0.0009611Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis1Highly InformativeInherited
DomainTransit peptide0.000007461Moderately InformativeDirect
DomainCBS domain0.000001027Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0005091InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)amino-acid metabolism0Least InformativeDirect
UniPathway (UP)aromatic compound metabolism0Least InformativeDirect
UniPathway (UP)cofactor metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0Moderately InformativeDirect
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)tryptophan metabolism0InformativeDirect
UniPathway (UP)aromatic amino-acid biosynthesis0InformativeDirect
UniPathway (UP)L-tryptophan biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism0Highly InformativeDirect
UniPathway (UP)L-threonine degradation0.0003708Highly InformativeDirect
UniPathway (UP)L-threonine biosynthesis0.0004269Highly InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR001926 SSF53686 Protein matches
Abstract

Pyridoxal-5'-phosphate-dependent enzymes (B6 enzymes) catalyze manifold reactions in the metabolism of amino acids. Most of these enzymes can be assigned to one of three different families of homologous proteins, the alpha, beta and gamma families. The alpha and gamma family might be distantly related with one another, but are clearly not homologous with the beta family. The beta family includes L- and D-serine dehydratase, threonine dehydratase, the beta subunit of tryptophan synthase, threonine synthase and cysteine synthase. These enzymes catalyze beta-replacement or beta-elimination reactions [PubMed8112347].

Comparison of sequences from eukaryotic, archebacterial, and eubacterial species indicates that the functional specialization of most B6 enzymes has occurred already in the universal ancestor cell. The cofactor pyridoxal-5-phosphate must have emerged very early in biological evolution; conceivably, organic cofactors and metal ions were the first biological catalysts [PubMed10800595].

The 3D structure of the beta-subunit of tryptophan synthase has been solved. The subunit has two domains that are approximately the same size and similar to each other in folding pattern. Each has a core containing a four-stranded parallel beta-sheet with three helices on its inner side and one on the outer side. The cofactor is bound at the interface between the domains [PubMed7748903].


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) · 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 22 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 Tryptophan synthase beta subunit-like PLP-dependent enzymes 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 22 hidden Markov models representing the Tryptophan synthase beta subunit-like PLP-dependent enzymes 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) · 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 ]