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 (3,009) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 21,387 49,144 39
Proteins 21,299 49,081 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 process8.087e-051.384e-06Least InformativeDirect
Biological Process (BP)single-organism metabolic process1.137e-120Least InformativeDirect
Biological Process (BP)cellular aromatic compound metabolic process11Least InformativeInherited
Biological Process (BP)organic cyclic 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 process7.109e-130Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process3.394e-090Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process9.612e-055.554e-10Moderately InformativeDirect
Biological Process (BP)cellular nitrogen compound biosynthetic process0.72160.664Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.70590.6561Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.55140.6378Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.79730.76Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process1.131e-055.115e-05InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process1.626e-090InformativeDirect
Biological Process (BP)cellular biogenic amine metabolic process0.019541.92e-07InformativeInherited
Biological Process (BP)regulation of hormone levels0.016890.00588InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.0015570.01508InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.85970.002836InformativeInherited
Biological Process (BP)serine family amino acid metabolic process06.728e-13Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process5.272e-051.362e-06Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.0002423.001e-10Highly InformativeDirect
Biological Process (BP)hormone biosynthetic process0.030230.009654Highly InformativeInherited
Biological Process (BP)cellular hormone metabolic process0.03410.00536Highly InformativeInherited
Molecular Function (MF)binding0.75441Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)anion binding0.00010577.201e-05Moderately InformativeDirect
Molecular Function (MF)isomerase activity0.00017640.00112Moderately InformativeInherited
Molecular Function (MF)racemase and epimerase activity1.362e-131.055e-13InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)nucleotide binding0.0020140.02223InformativeInherited
Molecular Function (MF)carboxylic acid binding0.27140.007444InformativeInherited
Molecular Function (MF)purine ribonucleoside binding0.00044960.002877InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.67630.8774InformativeInherited
Molecular Function (MF)hydro-lyase activity11InformativeInherited
Molecular Function (MF)ATP binding2.29e-070.0001664Highly InformativeDirect
Molecular Function (MF)amino acid binding5.661e-061.949e-09Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity0.0081020.008526Highly 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 1.384e-06 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
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 amino acid metabolic process 0 Moderately Informative Direct
Biological Process (BP) sulfur compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 5.554e-10 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.6378 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.76 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6561 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.664 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 5.115e-05 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 1.92e-07 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.00588 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.01508 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.002836 Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 6.728e-13 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 3.695e-06 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 1.362e-06 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 3.001e-10 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 0.009654 Highly Informative Inherited
Biological Process (BP) cellular hormone metabolic process 0.00536 Highly Informative Inherited
Biological Process (BP) tryptophan metabolic process 0.9225 Highly Informative Inherited
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) lyase activity 0 Moderately Informative Direct
Molecular Function (MF) anion binding 7.201e-05 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0.00112 Moderately Informative Inherited
Molecular Function (MF) racemase and epimerase activity 1.055e-13 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.02223 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.007444 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.002877 Informative Inherited
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.8774 Informative Inherited
Molecular Function (MF) hydro-lyase activity 1 Informative Inherited
Molecular Function (MF) ATP binding 0.0001664 Highly Informative Direct
Molecular Function (MF) amino acid binding 1.949e-09 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0.008526 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 0.0008312 Informative Direct
Cellular Component (CC) chloroplast stroma 3.099e-05 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)nutrient utilization0.01949Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source7.056e-07InformativeDirect

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 bonds0.0006183Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Racemases and epimerases0.3924InformativeInherited
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 derivatives0.0256Highly InformativeInherited
Enzyme Commission (EC)Acting on phosphates1Highly 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 processGluconeogenesis0.0002175Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis1Highly InformativeInherited
DomainCBS domain6.771e-07Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0001898InformativeDirect

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)cofactor metabolism0.777Least InformativeInherited
UniPathway (UP)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)L-cysteine biosynthesis0Highly InformativeDirect
UniPathway (UP)coenzyme M biosynthesis0Highly 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 ]