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beta-lactamase/transpeptidase-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   beta-lactamase/transpeptidase-like [ 56600]
Superfamily:   beta-lactamase/transpeptidase-like [ 56601] (3)
Families:   beta-Lactamase/D-ala carboxypeptidase [ 56602] (18)
  Glutaminase [ 90084] (2)
  Dac-like [ 144040] (3)

Superfamily statistics
Genomes (2,250) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 23,545 91,562 111
Proteins 23,353 91,079 111

 Functional annotation
General category Metabolism
Detailed category Other enzymes

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 process0.032812.613e-09Least InformativeInherited
Biological Process (BP)biosynthetic process0.95115.635e-05Least InformativeInherited
Biological Process (BP)response to stimulus0.68831Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.910.3567Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.2048.437e-05Least InformativeInherited
Biological Process (BP)single-organism cellular process0.44060.2975Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.26292.503e-08Least InformativeInherited
Biological Process (BP)multicellular organismal process0.90671Least InformativeInherited
Biological Process (BP)carbohydrate derivative metabolic process0.0039570Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0046172.034e-13Moderately InformativeInherited
Biological Process (BP)multi-organism process0.15740.3247Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.011672.705e-13Moderately InformativeInherited
Biological Process (BP)cellular catabolic process0.02060.109Moderately InformativeInherited
Biological Process (BP)organic substance catabolic process0.067330.2209Moderately InformativeInherited
Biological Process (BP)cellular amino acid metabolic process0.032280.003605Moderately InformativeInherited
Biological Process (BP)organonitrogen compound biosynthetic process0.20171.046e-12Moderately InformativeInherited
Biological Process (BP)regulation of multicellular organismal process0.088520.8771Moderately InformativeInherited
Biological Process (BP)system process0.043430.1388Moderately InformativeInherited
Biological Process (BP)synaptic transmission0.00051830.0004021InformativeDirect
Biological Process (BP)glutamine family amino acid metabolic process3.717e-077.355e-10InformativeDirect
Biological Process (BP)carboxylic acid catabolic process0.0051844.029e-06InformativeInherited
Biological Process (BP)organonitrogen compound catabolic process0.0520.2767InformativeInherited
Biological Process (BP)regulation of system process0.00079020.004278InformativeInherited
Biological Process (BP)aminoglycan biosynthetic process8.402e-090Highly InformativeDirect
Biological Process (BP)feeding behavior1.253e-062.196e-07Highly InformativeDirect
Biological Process (BP)glutamine family amino acid catabolic process6.508e-051.683e-09Highly InformativeDirect
Biological Process (BP)glycosaminoglycan metabolic process3.98e-120Highly InformativeDirect
Biological Process (BP)cell wall biogenesis2.885e-070Highly InformativeDirect
Biological Process (BP)cell wall macromolecule metabolic process6.403e-080Highly InformativeDirect
Biological Process (BP)multi-organism behavior7.656e-062.102e-06Highly InformativeDirect
Biological Process (BP)cellular component macromolecule biosynthetic process1.05e-090Highly InformativeDirect
Molecular Function (MF)hydrolase activity8.455e-098.537e-11Least InformativeDirect
Molecular Function (MF)binding10.4607Least InformativeInherited
Molecular Function (MF)anion binding0.062532.673e-11Moderately InformativeInherited
Molecular Function (MF)organic cyclic compound binding0.20730.0008762Moderately InformativeInherited
Molecular Function (MF)heterocyclic compound binding0.1820.0006907Moderately InformativeInherited
Molecular Function (MF)carboxylic acid binding0.00020640InformativeDirect
Molecular Function (MF)hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides0.12690.01005InformativeInherited
Molecular Function (MF)drug binding2.339e-050Highly InformativeDirect
Molecular Function (MF)monocarboxylic acid binding1.926e-050Highly InformativeDirect
Molecular Function (MF)sulfur compound binding9.503e-060Highly InformativeDirect

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 2.613e-09 Least Informative Direct
Biological Process (BP) biosynthetic process 5.635e-05 Least Informative Direct
Biological Process (BP) single-organism metabolic process 2.503e-08 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 8.437e-05 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.3567 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.2975 Least Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 2.034e-13 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 2.705e-13 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound biosynthetic process 1.046e-12 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.3247 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.8353 Moderately Informative Inherited
Biological Process (BP) organ development 0.9714 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.1371 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2209 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.109 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.296 Moderately Informative Inherited
Biological Process (BP) cellular amino acid metabolic process 0.003605 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8771 Moderately Informative Inherited
Biological Process (BP) system process 0.1388 Moderately Informative Inherited
Biological Process (BP) synaptic transmission 0.0004021 Informative Direct
Biological Process (BP) glutamine family amino acid metabolic process 7.355e-10 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 4.029e-06 Informative Direct
Biological Process (BP) regulation of anatomical structure morphogenesis 0.003756 Informative Inherited
Biological Process (BP) organonitrogen compound catabolic process 0.2767 Informative Inherited
Biological Process (BP) organ morphogenesis 0.0214 Informative Inherited
Biological Process (BP) regulation of system process 0.004278 Informative Inherited
Biological Process (BP) aminoglycan biosynthetic process 0 Highly Informative Direct
Biological Process (BP) feeding behavior 2.196e-07 Highly Informative Direct
Biological Process (BP) glutamine family amino acid catabolic process 1.683e-09 Highly Informative Direct
Biological Process (BP) regulation of cell morphogenesis 4.943e-05 Highly Informative Direct
Biological Process (BP) glycosaminoglycan metabolic process 0 Highly Informative Direct
Biological Process (BP) cell wall biogenesis 0 Highly Informative Direct
Biological Process (BP) cell wall macromolecule metabolic process 0 Highly Informative Direct
Biological Process (BP) post-embryonic organ development 8.072e-06 Highly Informative Direct
Biological Process (BP) multi-organism behavior 2.102e-06 Highly Informative Direct
Biological Process (BP) cellular component macromolecule biosynthetic process 0 Highly Informative Direct
Biological Process (BP) post-embryonic development 0.002631 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 8.537e-11 Least Informative Direct
Molecular Function (MF) binding 0.4607 Least Informative Inherited
Molecular Function (MF) transferase activity 1 Least Informative Inherited
Molecular Function (MF) anion binding 2.673e-11 Moderately Informative Direct
Molecular Function (MF) organic cyclic compound binding 0.0008762 Moderately Informative Direct
Molecular Function (MF) heterocyclic compound binding 0.0006907 Moderately Informative Direct
Molecular Function (MF) peptidase activity 4.972e-05 Informative Direct
Molecular Function (MF) transferase activity, transferring glycosyl groups 0.0002182 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 0.01005 Informative Inherited
Molecular Function (MF) drug binding 0 Highly Informative Direct
Molecular Function (MF) exopeptidase activity 3.258e-12 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) sulfur compound binding 0 Highly Informative Direct
Molecular Function (MF) serine-type peptidase activity 0.001195 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)In linear amides2.368e-16Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.259Moderately InformativeInherited
Enzyme Commission (EC)In cyclic amides0InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.001912InformativeInherited
Enzyme Commission (EC)Serine-type carboxypeptidases0Highly InformativeDirect
Enzyme Commission (EC)Peptidoglycan glycosyltransferase0Highly InformativeDirect
Enzyme Commission (EC)Beta-lactamase0Highly InformativeDirect

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)pericellular component development variant4.838e-05Moderately InformativeDirect
Worm Phenotype (WP)basement membrane remodeling variant1.99e-05InformativeDirect

Document: WP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Acting on carbon-nitrogen bonds, other than peptide bonds0Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases0.2606Moderately InformativeInherited
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Moderately InformativeInherited
Enzyme Commission (EC)In linear amides2.399e-16InformativeDirect
Enzyme Commission (EC)Hexosyltransferases5.332e-05InformativeDirect
Enzyme Commission (EC)In cyclic amides0Highly InformativeDirect
Enzyme Commission (EC)Aminopeptidases0.00182Highly InformativeInherited

Document: EC annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use3.83e-05Moderately InformativeDirect
Drugbank ATC_code (DB)other beta-lactam antibacterials0.0003644Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0.000947Moderately InformativeDirect
Biological processAntibiotic resistance0InformativeDirect
Biological processCell shape0InformativeDirect
Biological processCell wall biogenesis/degradation0InformativeDirect
Biological processSporulation2.151e-07InformativeDirect
Cellular componentMembrane1.065e-05Least InformativeDirect
Cellular componentCell membrane0Moderately InformativeDirect
Cellular componentPeriplasm3.994e-10InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane1Least InformativeInherited
DomainSignal-anchor0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationGlycosyltransferase0InformativeDirect
Post-translational modificationCarboxypeptidase4.816e-14Highly InformativeDirect
Post-translational modificationAminopeptidase0.0003545Highly InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)cell wall metabolism0Moderately InformativeDirect
UniPathway (UP)cellular component biogenesis0Moderately InformativeDirect
UniPathway (UP)peptidoglycan biosynthesis0InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR012338 SSF56601 Protein matches
Abstract

This entry represents a beta-lactamase structural motif, which contins a cluster of alpha-helices and an alpha/beta sandwich. In addition to beta-lactamases, this domain is also found in D-ala carboxypeptidase/transpeptidase, esterase (EstB) [PubMed11847270], the penicillin receptor BlaR (C-terminal domain), D-aminopeptidase (N-terminal domain) [PubMed10986464], penicillin-biding proteins (e.g. PBP2x, PBP5), and in glutaminase (GlnA). Beta-lactamases are the most common bacterial resistance mechanism against beta-lactam antibiotics [PubMed12945052]. Beta-lactamases appear to have evolved from DD-transpeptidases, which are penicillin-binding proteins involved in cell wall biosynthesis, and as such are one of the main targets of beta-lactam antibiotics.


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) · 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 43 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 beta-lactamase/transpeptidase-like 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 43 hidden Markov models representing the beta-lactamase/transpeptidase-like 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) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · 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.