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 (3,050) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 21,810 117,865 39
Proteins 21,694 117,766 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 process5.877e-061.155e-07Least InformativeDirect
Biological Process (BP)single-organism metabolic process5.349e-140Least 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)multicellular organismal process0.91191Least InformativeInherited
Biological Process (BP)cellular amino acid metabolic process00Moderately InformativeDirect
Biological Process (BP)sulfur compound metabolic process1.012e-130Moderately InformativeDirect
Biological Process (BP)single-organism biosynthetic process2.209e-110Moderately InformativeDirect
Biological Process (BP)organonitrogen compound biosynthetic process4.147e-061.163e-11Moderately InformativeDirect
Biological Process (BP)multi-organism process0.35070.889Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.56060.8666Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.73060.6665Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.56370.6432Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.81920.777Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.74890.6795Moderately InformativeInherited
Biological Process (BP)monocarboxylic acid metabolic process11Moderately InformativeInherited
Biological Process (BP)sulfur amino acid metabolic process1.492e-061.833e-06InformativeDirect
Biological Process (BP)sulfur compound biosynthetic process4.165e-100InformativeDirect
Biological Process (BP)multi-multicellular organism process0.00042060.0008683InformativeDirect
Biological Process (BP)cellular biogenic amine metabolic process0.0042942.087e-08InformativeInherited
Biological Process (BP)regulation of hormone levels0.014770.006287InformativeInherited
Biological Process (BP)alpha-amino acid biosynthetic process0.00020350.004989InformativeInherited
Biological Process (BP)aspartate family amino acid metabolic process0.97360.01443InformativeInherited
Biological Process (BP)serine family amino acid metabolic process03.752e-15Highly InformativeDirect
Biological Process (BP)cellular biogenic amine biosynthetic process3.244e-065.764e-07Highly InformativeDirect
Biological Process (BP)indole-containing compound biosynthetic process0.00011979.663e-11Highly InformativeDirect
Biological Process (BP)sulfur compound catabolic process0.00085237.419e-05Highly InformativeDirect
Biological Process (BP)cellular hormone metabolic process0.042070.006202Highly InformativeInherited
Molecular Function (MF)binding0.38171Least InformativeInherited
Molecular Function (MF)lyase activity00Moderately InformativeDirect
Molecular Function (MF)isomerase activity7.844e-050.0005791Moderately InformativeDirect
Molecular Function (MF)anion binding2.863e-063.535e-06Moderately InformativeDirect
Molecular Function (MF)racemase and epimerase activity5.177e-158.971e-15InformativeDirect
Molecular Function (MF)cofactor binding00InformativeDirect
Molecular Function (MF)nucleotide binding0.00062180.01028InformativeInherited
Molecular Function (MF)carboxylic acid binding0.30040.01044InformativeInherited
Molecular Function (MF)purine ribonucleoside binding0.00010490.001008InformativeInherited
Molecular Function (MF)purine ribonucleoside triphosphate binding0.8951InformativeInherited
Molecular Function (MF)hydro-lyase activity11InformativeInherited
Molecular Function (MF)ATP binding2.555e-084.086e-05Highly InformativeDirect
Molecular Function (MF)amino acid binding2.437e-071.141e-10Highly InformativeDirect
Molecular Function (MF)pyridoxal phosphate binding00Highly InformativeDirect
Molecular Function (MF)carbon-sulfur lyase activity0.0091480.003128Highly InformativeInherited
Molecular Function (MF)carbon-oxygen lyase activity, acting on phosphates0.48370.706Highly 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 1.155e-07 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) multicellular organismal 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 1.163e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.889 Moderately Informative Inherited
Biological Process (BP) reproduction 0.7399 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.8666 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.6432 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.777 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.6665 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.6795 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 1 Moderately Informative Inherited
Biological Process (BP) sulfur amino acid metabolic process 1.833e-06 Informative Direct
Biological Process (BP) cellular biogenic amine metabolic process 2.087e-08 Informative Direct
Biological Process (BP) sulfur compound biosynthetic process 0 Informative Direct
Biological Process (BP) multi-multicellular organism process 0.0008683 Informative Direct
Biological Process (BP) cellular modified amino acid metabolic process 1 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.006287 Informative Inherited
Biological Process (BP) alpha-amino acid biosynthetic process 0.004989 Informative Inherited
Biological Process (BP) aspartate family amino acid metabolic process 0.01443 Informative Inherited
Biological Process (BP) serine family amino acid metabolic process 3.752e-15 Highly Informative Direct
Biological Process (BP) aromatic amino acid family biosynthetic process 1.319e-06 Highly Informative Direct
Biological Process (BP) cellular biogenic amine biosynthetic process 5.764e-07 Highly Informative Direct
Biological Process (BP) indole-containing compound biosynthetic process 9.663e-11 Highly Informative Direct
Biological Process (BP) sulfur compound catabolic process 7.419e-05 Highly Informative Direct
Biological Process (BP) hormone biosynthetic process 0.01224 Highly Informative Inherited
Biological Process (BP) cellular hormone metabolic process 0.006202 Highly Informative Inherited
Biological Process (BP) tryptophan metabolic process 0.8447 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 0.0005791 Moderately Informative Direct
Molecular Function (MF) anion binding 3.535e-06 Moderately Informative Direct
Molecular Function (MF) racemase and epimerase activity 8.971e-15 Informative Direct
Molecular Function (MF) cofactor binding 0 Informative Direct
Molecular Function (MF) nucleotide binding 0.01028 Informative Inherited
Molecular Function (MF) carboxylic acid binding 0.01044 Informative Inherited
Molecular Function (MF) purine ribonucleoside binding 0.001008 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 4.086e-05 Highly Informative Direct
Molecular Function (MF) amino acid binding 1.141e-10 Highly Informative Direct
Molecular Function (MF) pyridoxal phosphate binding 0 Highly Informative Direct
Molecular Function (MF) carbon-sulfur lyase activity 0.003128 Highly Informative Inherited
Molecular Function (MF) carbon-oxygen lyase activity, acting on phosphates 0.706 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 0.0007004 Informative Direct
Cellular Component (CC) chloroplast stroma 3.177e-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)metabolism and growth0.5495Least InformativeInherited
Yeast Phenotype (YP)nutrient utilization0.02012Moderately InformativeInherited
Yeast Phenotype (YP)utilization of nitrogen source7.131e-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 bonds0.0005165Moderately InformativeDirect
Enzyme Commission (EC)Isomerases1Moderately InformativeInherited
Enzyme Commission (EC)Carbon-nitrogen lyases0InformativeDirect
Enzyme Commission (EC)Racemases and epimerases0.3851InformativeInherited
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 derivatives0.02482Highly 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 processGluconeogenesis0.0002159Highly InformativeDirect
Biological processBranched-chain amino acid biosynthesis1Highly InformativeInherited
DomainTransit peptide9.732e-05Moderately InformativeDirect
DomainCBS domain7.005e-07Highly InformativeDirect
Molecular functionPyridoxal phosphate0Highly InformativeDirect
Post-translational modificationLyase0Moderately InformativeDirect
Post-translational modificationS-nitrosylation0.0002482InformativeDirect

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)proteinogenic amino-acid biosynthesis0Moderately InformativeDirect
UniPathway (UP)cofactor biosynthesis0.4593Moderately InformativeInherited
UniPathway (UP)L-cysteine metabolism0InformativeDirect
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 ]