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2  structures 14  species 0  interactions 14  sequences 2  architectures

Family: Lactamase_B_5 (PF14597)

Summary: Metallo-beta-lactamase superfamily

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This is the Wikipedia entry entitled "Metallo-beta-lactamase protein fold". More...

Metallo-beta-lactamase protein fold Edit Wikipedia article

Metallo-beta-lactamase superfamily
1BMC.png
Cartoon diagram of the crystallographic structure of a zinc metallo-beta-lactamase from bacillus cereus (N-terminus = blue, C-terminus = blue) The catalytic zinc ion is depicted as a grey sphere.[1]
Identifiers
Symbol Lactamase_B
Pfam PF00753
InterPro IPR001279
SCOP 1bmc
SUPERFAMILY 1bmc

The metallo-beta-lactamase protein fold is a protein domain contained in class B beta-lactamases and a number of other proteins .[1] These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.

Metallo-beta-lactamases are important enzymes because they are involved in the breakdown of antibiotics by antibiotic-resistant bacteria.[2]

See also[edit]

References[edit]

  1. ^ a b PDB 1bmc ; Carfi A, Pares S, Duée E, Galleni M, Duez C, Frère JM, Dideberg O (October 1995). "The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold". EMBO J. 14 (20): 4914–21. PMC 394593. PMID 7588620. 
  2. ^ "Shaw, Robert W. (Lubbock, TX, US), Kim, Sung-kun (Lubbock, TX, US)" ("November" "2008"). "Inhibition of metallo-β-lactamase" ("7456274"). 

This article incorporates text from the public domain Pfam and InterPro IPR001279

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Metallo-beta-lactamase superfamily Provide feedback

This is a small family of putative metal-dependent hydrolases.

External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Metallo-HOrase (CL0381), which has the following description:

This superfamily of enzymes including beta-lactamases, thiolesterases, members of the glyoxalase II family that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid all bind two ions of zinc. An additional family of competence proteins essential for natural transformation do not appear to bind zinc, and might be a transporter involved in DNA uptake.

The clan contains the following 7 members:

DUF2070 Lactamase_B Lactamase_B_2 Lactamase_B_3 Lactamase_B_4 Lactamase_B_5 PDEase_II

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(4)
Full
(14)
Representative proteomes NCBI
(21)
Meta
(24)
RP15
(0)
RP35
(2)
RP55
(5)
RP75
(5)
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Format an alignment

  Seed
(4)
Full
(14)
Representative proteomes NCBI
(21)
Meta
(24)
RP15
(0)
RP35
(2)
RP55
(5)
RP75
(5)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(4)
Full
(14)
Representative proteomes NCBI
(21)
Meta
(24)
RP15
(0)
RP35
(2)
RP55
(5)
RP75
(5)
Raw Stockholm Download   Download     Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

This family is new in this Pfam release.

Seed source: CATH:2p97A00
Previous IDs: none
Type: Domain
Author: Coggill P
Number in seed: 4
Number in full: 14
Average length of the domain: 190.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 92.85 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.4 28.4
Trusted cut-off 28.8 28.7
Noise cut-off 28.3 28.0
Model length: 199
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Lactamase_B_5 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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