SUPERFAMILY 1.75 HMM library and genome assignments server

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 (3,052) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,840 117,865 39
Proteins 21,723 117,766 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)nitrogen compound metabolic process00Least InformativeDirect
Biological Process (BP)biosynthetic process0.00000063060.00000001185Least InformativeDirect
Biological Process (BP)single-organism metabolic process00Least InformativeDirect
Biological Process (BP)single-organism cellular process0.0000027790.00000003962Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process11Least InformativeInherited
Biological Process (BP)multicellular organismal process0.90531Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)heterocycle metabolic process11Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process0.0000000000000032510Moderately InformativeDirect
Biological Process (BP)small molecule biosynthetic process0.000000002110.00000000000001414Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process0.00000038840.0000000000005298Moderately InformativeDirect
Biological Process (BP)heterocycle biosynthetic process0.84430.7992Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.69310.7775Moderately InformativeInherited
Biological Process (BP)multi-organism process0.60391Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.91540.8985Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.85330.8039Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.30261Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process0.000000055040.00000003333InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process0.0000000000086080InformativeDirect
Biological Process (BP)multi-multicellular organism process0.0004590.0009239InformativeDirect
Biological Process (BP)cellular biogenic amine metabolic process0.0045030.00000002103InformativeInherited
Biological Process (BP)regulation of hormone levels0.015510.006438InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.000029170.001371InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process10.02733InformativeInherited
Biological Process (BP)serine family amino acid metabolic process00Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process0.000003240.000000547Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.00020850.0000000001611Highly InformativeDirect
Biological Process (BP)cellular hormone metabolic process0.047340.006575Highly InformativeInherited
Molecular Function (MF)binding0.45681Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.00011660.0007461Moderately InformativeDirect
Molecular Function (MF)anion binding0.0000024740.000003529Moderately InformativeDirect
Molecular Function (MF)small molecule binding0.0061510.0002462Moderately InformativeInherited
Molecular Function (MF)carbohydrate derivative binding0.0046210.02241Moderately InformativeInherited
Molecular Function (MF)racemase and epimerase activity0.000000000000006470.00000000000001064InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)nucleotide binding0.10511InformativeInherited
Molecular Function (MF)carboxylic acid binding0.29780.01095InformativeInherited
Molecular Function (MF)purine ribonucleoside binding0.00011660.001051InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.89491InformativeInherited
Molecular Function (MF)hydro-lyase activity11InformativeInherited
Molecular Function (MF)ATP binding0.000000028980.00004354Highly InformativeDirect
Molecular Function (MF)amino acid binding0.00000026960.0000000001415Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity0.0047920.001429Highly InformativeInherited
Molecular Function (MF)carbon-oxygen lyase activity, acting on phosphates0.52170.7477Highly 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) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.00000001185 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00000003962 Least Informative Direct
Biological Process (BP) multicellular organismal process 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 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 0.00000000000001414 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 0.0000000000005298 Moderately Informative Direct
Biological Process (BP) multi-organism process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.9075 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.8985 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.8039 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.7775 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.7992 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 0.00000003333 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 0.00000002103 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) multi-multicellular organism process 0.0009239 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.006438 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.02733 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.001371 Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 0 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 0.000001836 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 0.000000547 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 0.0000000001611 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 0.0147 Highly Informative Inherited
Biological Process (BP) cellular hormone metabolic process 0.006575 Highly Informative Inherited
Biological Process (BP) tryptophan metabolic process 0.9036 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.0007461 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0002462 Moderately Informative Direct
Molecular Function (MF) anion binding 0.000003529 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.02241 Moderately Informative Inherited
Molecular Function (MF) racemase and epimerase activity 0.00000000000001064 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 1 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.01095 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.001051 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 1 Informative Inherited
Molecular Function (MF) hydro-lyase activity 1 Informative Inherited
Molecular Function (MF) ATP binding 0.00004354 Highly Informative Direct
Molecular Function (MF) amino acid binding 0.0000000001415 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0.001429 Highly Informative Inherited
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0.7477 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) plastid 0.0007161 Informative Direct
Cellular Component (CC) chloroplast stroma 0.00003248 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)growth variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.05925Least InformativeInherited
Worm Phenotype (WP)chemical response variant0.002587Moderately InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)metabolism and growth0.5527Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.02022Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source0.0000007147InformativeDirect

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)viscus0Least InformativeDirect

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 stage0.0003473InformativeDirect

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 bonds0.0005088Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0.3836InformativeInherited
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 derivatives0.02472Highly InformativeInherited
Enzyme Commission (EC)Carbon-sulfur lyases1Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)alimentary tract and metabolism0Least InformativeDirect
Drugbank ATC_code (DB)other plain vitamin preparations1Moderately InformativeInherited
Drugbank ATC_code (DB)pyridoxine (vit b6)0InformativeDirect
Drugbank ATC_code (DB)pyridoxal phosphate0InformativeDirect

Document: DB 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 processGluconeogenesis0.000215Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis1Highly InformativeInherited
DomainTransit peptide0.0001006Moderately InformativeDirect
DomainCBS domain0.0000007098Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0002478InformativeDirect

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)carbohydrate metabolism1Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)aromatic compound biosynthesis0Moderately InformativeDirect
UniPathway (UP)carbohydrate biosynthesis0.08614Moderately InformativeInherited
UniPathway (UP)amino-acid degradation1Moderately InformativeInherited
UniPathway (UP)tryptophan metabolism0InformativeDirect
UniPathway (UP)aromatic amino-acid biosynthesis0InformativeDirect
UniPathway (UP)gluconeogenesis0.0009387InformativeDirect
UniPathway (UP)L-tryptophan biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0Highly InformativeDirect
UniPathway (UP)L-cysteine metabolism0Highly InformativeDirect
UniPathway (UP)L-threonine degradation0.0003739Highly InformativeDirect
UniPathway (UP)L-threonine biosynthesis0.0004172Highly 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) · DrugBank ATC (DB) · 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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]