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 | |||||||||||
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![]() Cartoon diagram of the crystallographic structure of a zinc metallo-beta-lactamase from bacillus cereus (N-terminus = blue, C-terminus = red) The catalytic zinc ion is depicted as a grey sphere.[1] | |||||||||||
Identifiers | |||||||||||
Symbol | Lactamase_B | ||||||||||
Pfam | PF00753 | ||||||||||
InterPro | IPR001279 | ||||||||||
SCOPe | 1bmc / SUPFAM | ||||||||||
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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] It is unclear whether metallo-beta-lactamase activity evolved once or twice within the superfamily; if twice, this would suggest structural exaptation.[3]
See also
References
- ^ 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. doi:10.1002/j.1460-2075.1995.tb00174.x. PMC 394593. PMID 7588620.
- ^ Shaw, Robert W; Kim, Sung-kun (November 2008). "Inhibition of metallo-β-lactamase". 7456274.
- ^ Alderson R, Barker D, Mitchell JB (2014). "One origin for metallo-beta-lactamase activity, or two? An investigation assessing a diverse set of reconstructed ancestral sequences based on a sample of phylogenetic trees". J. Mol. Evol. 79 (3–4): 117–29. doi:10.1007/s00239-014-9639-7. PMC 4185109. PMID 25185655.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Metallo-beta-lactamase superfamily Provide feedback
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Literature references
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Neuwald AF, Liu JS, Lipman DJ, Lawrence CE; , Nucleic Acids Res 1997;25:1665-1677.: Extracting protein alignment models from the sequence database. PUBMED:9108146 EPMC:9108146
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Carfi A, Pares S, Duee E, Galleni M, Duez C, Frere JM, Dideberg O; , EMBO J 1995;14:4914-4921.: The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. PUBMED:7588620 EPMC:7588620
Internal database links
SCOOP: | Beta-Casp Beta_lactamase3 BLACT_WH HAGH_C Lactamase_B_2 Lactamase_B_3 Lactamase_B_4 Lactamase_B_5 Lactamase_B_6 PDEase_II |
Similarity to PfamA using HHSearch: | Lactamase_B_2 Lactamase_B_3 Lactamase_B_6 |
External database links
HOMSTRAD: | blmb |
SCOP: | 1bme |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001279
Apart from the beta-lactamases and metallo-beta-lactamases, a number of other proteins contain this domain [PUBMED:7588620]. 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.
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 9 members:
Beta_lactamase3 HAGH_C Lactamase_B Lactamase_B_2 Lactamase_B_3 Lactamase_B_4 Lactamase_B_5 Lactamase_B_6 PDEase_IIAlignments
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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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 (126) |
Full (67352) |
Representative proteomes | UniProt (289346) |
NCBI (508857) |
Meta (11463) |
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RP15 (7979) |
RP35 (30792) |
RP55 (65229) |
RP75 (112328) |
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Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (126) |
Full (67352) |
Representative proteomes | UniProt (289346) |
NCBI (508857) |
Meta (11463) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (7979) |
RP35 (30792) |
RP55 (65229) |
RP75 (112328) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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
Seed source: | [1] |
Previous IDs: | lactamase_B; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Ponting CP |
Number in seed: | 126 |
Number in full: | 67352 |
Average length of the domain: | 184.20 aa |
Average identity of full alignment: | 14 % |
Average coverage of the sequence by the domain: | 50.73 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 197 | ||||||||||||
Family (HMM) version: | 28 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There are 15 interactions for this family. More...
RMMBL Choline_bind_1 Lactamase_B RMMBL Alkyl_sulf_dimr Alkyl_sulf_dimr Flavodoxin_1 Beta-Casp Beta-Casp Rhodanese KH_2 Flavodoxin_1 Alkyl_sulf_C Alkyl_sulf_C RhodaneseStructures
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 domain has been found. There are 812 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 sequence.
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