SUPERFAMILY 1.75 HMM library and genome assignments server

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Penicillin-binding protein associated domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   Penicillin-binding protein associated domain [ 69188]
Superfamily:   Penicillin-binding protein associated domain [ 69189] (2)
Families:   PBP5 C-terminal domain-like [ 69190] (2)
  Pencillin binding protein 4 (PbpD), C-terminal domain [ 110098]


Superfamily statistics
Genomes (1,418) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 2,247 17,707 4
Proteins 2,247 17,705 4


Functional annotation
General category Other
Detailed category Unknown function

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Serine-type carboxypeptidases0Highly InformativeDirect

Document: EC 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 peptide bonds (peptidases)0Moderately InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR015956 SSF69189 Protein matches
Abstract

This entry represents a structural motif found at the C-terminal of penicillin-binding proteins 4 (PBP4) and 5 (PBP5), as well as at the C-terminal of D-Ala-D-Ala carboxypeptidase A, a member of the MEROPS S11 peptidase family (PBP4 and PBP5 also belong to this peptidase family). These domains share a similar structure, consisting of a beta-sandwich of six strands in two sheets [PubMed14555648, PubMed15596446].

Penicillin-binding proteins are beta-lactam antibiotic-sensitive bacterial enzymes required for the growth and maintenance of the peptidoglycan layer of the bacterial cell wall that protects the cell from osmotic stress. PBP4 functions as a transpeptidase, acting co-operatively with PBP2 in staphylococcal cell wall biosynthesis and susceptibility to antimicrobial agents [PubMed16411754].


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 · Enzyme Commission (EC) · Enzyme Commission (EC) ]

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 3 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 Penicillin-binding protein associated domain 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 3 hidden Markov models representing the Penicillin-binding protein associated domain 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 · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]