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910  structures 8791  species 0  interactions 77989  sequences 561  architectures

Family: Lactamase_B (PF00753)

Summary: Metallo-beta-lactamase superfamily

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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 = red) The catalytic zinc ion is depicted as a grey sphere.[1]
Identifiers
SymbolLactamase_B
PfamPF00753
InterProIPR001279
SCOPe1bmc / SUPFAM

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

  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. doi:10.1002/j.1460-2075.1995.tb00174.x. PMC 394593. PMID 7588620.
  2. ^ Shaw, Robert W; Kim, Sung-kun (November 2008). "Inhibition of metallo-β-lactamase". 7456274.
  3. ^ 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.
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.

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

  1. 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

  2. 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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001279

Metallo beta lactamases exhibit low sequence identity between enzymes but they are structurally similar. They have a characteristic alpha-beta/beta-alpha sandwich fold in which the active site is at the interface between domains. Apart from the beta-lactamases and metallo-beta-lactamases, a number of other proteins contain this domain and share the same fold type [ PUBMED:7588620 , PUBMED:23163348 ]. 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 10 members:

Beta_lactamase3 HAGH_C Lactamase_B Lactamase_B_2 Lactamase_B_3 Lactamase_B_4 Lactamase_B_5 Lactamase_B_6 ODP 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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(123)
Full
(77989)
Representative proteomes UniProt
(340066)
RP15
(9733)
RP35
(36180)
RP55
(76632)
RP75
(129422)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(123)
Full
(77989)
Representative proteomes UniProt
(340066)
RP15
(9733)
RP35
(36180)
RP55
(76632)
RP75
(129422)
Alignment:
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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
(123)
Full
(77989)
Representative proteomes UniProt
(340066)
RP15
(9733)
RP35
(36180)
RP55
(76632)
RP75
(129422)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: [1]
Previous IDs: lactamase_B;
Type: Domain
Sequence Ontology: SO:0000417
Author: Ponting CP , Bateman A
Number in seed: 123
Number in full: 77989
Average length of the domain: 183.50 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 50.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.7 21.9
Trusted cut-off 22.7 21.9
Noise cut-off 22.6 21.8
Model length: 197
Family (HMM) version: 29
Download: download the raw HMM for this family

Species distribution

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Selections

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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 domain has been found. There are 910 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0ELP8 View 3D Structure Click here
A0A0R0FCE9 View 3D Structure Click here
A0A0R0H2K8 View 3D Structure Click here
A0A1D6H2V7 View 3D Structure Click here
A0A1D6I8T9 View 3D Structure Click here
A0A1D6K1V4 View 3D Structure Click here
A0A1D6NGC6 View 3D Structure Click here
A0A1D8PID4 View 3D Structure Click here
A4D2B0 View 3D Structure Click here
A4HZ66 View 3D Structure Click here
A4I0A3 View 3D Structure Click here
A4IAA8 View 3D Structure Click here
A4IAA9 View 3D Structure Click here
A5WWD2 View 3D Structure Click here
B0BNJ4 View 3D Structure Click here
B0R0T6 View 3D Structure Click here
B6U1D4 View 3D Structure Click here
B8A148 View 3D Structure Click here
C0H490 View 3D Structure Click here
C6TKG9 View 3D Structure Click here
D3ZB91 View 3D Structure Click here
D4A249 View 3D Structure Click here
D4A2F7 View 3D Structure Click here
F1M1E4 View 3D Structure Click here
F1QIZ3 View 3D Structure Click here
F1RBN6 View 3D Structure Click here
F6NM08 View 3D Structure Click here
G3V6W7 View 3D Structure Click here
H2KYX6 View 3D Structure Click here
I1KC49 View 3D Structure Click here
I1KUP5 View 3D Structure Click here
I1LJN3 View 3D Structure Click here
I1M2S7 View 3D Structure Click here
I1MB50 View 3D Structure Click here
I1MD49 View 3D Structure Click here
I6XHY3 View 3D Structure Click here
I6Y4A5 View 3D Structure Click here
K7KL53 View 3D Structure Click here
K7KLP6 View 3D Structure Click here
K7KUZ8 View 3D Structure Click here
K7LVE4 View 3D Structure Click here
K7MDN4 View 3D Structure Click here
O06154 View 3D Structure Click here
O07720 View 3D Structure Click here
O17598 View 3D Structure Click here
O17636 View 3D Structure Click here
O24495 View 3D Structure Click here
O24496 View 3D Structure Click here
O35952 View 3D Structure Click here
O53534 View 3D Structure Click here
O69728 View 3D Structure Click here
O86336 View 3D Structure Click here
O86346 View 3D Structure Click here
O94250 View 3D Structure Click here
O95571 View 3D Structure Click here
P0AC84 View 3D Structure Click here
P32717 View 3D Structure Click here
P37443 View 3D Structure Click here
P72062 View 3D Structure Click here
P75849 View 3D Structure Click here
P87168 View 3D Structure Click here
P9WLD7 View 3D Structure Click here
P9WMW3 View 3D Structure Click here
Q05584 View 3D Structure Click here
Q06224 View 3D Structure Click here
Q08347 View 3D Structure Click here
Q0JIR1 View 3D Structure Click here
Q10LW8 View 3D Structure Click here
Q11123 View 3D Structure Click here
Q12320 View 3D Structure Click here
Q16775 View 3D Structure Click here
Q17596 View 3D Structure Click here
Q20700 View 3D Structure Click here
Q2FV07 View 3D Structure Click here
Q2FXI3 View 3D Structure Click here
Q2FXY4 View 3D Structure Click here
Q2FY29 View 3D Structure Click here
Q2FZ19 View 3D Structure Click here
Q2FZG9 View 3D Structure Click here
Q2G1R6 View 3D Structure Click here
Q2G2U5 View 3D Structure Click here
Q46877 View 3D Structure Click here
Q4CK95 View 3D Structure Click here
Q4CPG0 View 3D Structure Click here
Q4D0L0 View 3D Structure Click here
Q4D587 View 3D Structure Click here
Q4D6D7 View 3D Structure Click here
Q4DNS8 View 3D Structure Click here
Q4DNS9 View 3D Structure Click here
Q4DW06 View 3D Structure Click here
Q4DYM2 View 3D Structure Click here
Q4E0K0 View 3D Structure Click here
Q53H82 View 3D Structure Click here
Q54EJ5 View 3D Structure Click here
Q54MR1 View 3D Structure Click here
Q54YG0 View 3D Structure Click here
Q561R9 View 3D Structure Click here
Q57626 View 3D Structure Click here
Q57744 View 3D Structure Click here
Q57749 View 3D Structure Click here
Q57890 View 3D Structure Click here
Q58142 View 3D Structure Click here
Q58158 View 3D Structure Click here
Q58271 View 3D Structure Click here
Q58298 View 3D Structure Click here
Q58633 View 3D Structure Click here
Q5QLQ5 View 3D Structure Click here
Q5U3T4 View 3D Structure Click here
Q682P6 View 3D Structure Click here
Q68D91 View 3D Structure Click here
Q69MU0 View 3D Structure Click here
Q69ZP3 View 3D Structure Click here
Q6AYD1 View 3D Structure Click here
Q6K9T9 View 3D Structure Click here
Q6NYF0 View 3D Structure Click here
Q6P963 View 3D Structure Click here
Q6PII5 View 3D Structure Click here
Q84JJ2 View 3D Structure Click here
Q86PD3 View 3D Structure Click here
Q8BL86 View 3D Structure Click here
Q8BWY4 View 3D Structure Click here
Q8I5Y8 View 3D Structure Click here
Q8IPU3 View 3D Structure Click here
Q8LDW8 View 3D Structure Click here
Q8MLZ3 View 3D Structure Click here
Q8MM62 View 3D Structure Click here
Q8N490 View 3D Structure Click here
Q8RWE1 View 3D Structure Click here
Q8VEB6 View 3D Structure Click here
Q8WT45 View 3D Structure Click here
Q95PY8 View 3D Structure Click here
Q95Q18 View 3D Structure Click here
Q99KB8 View 3D Structure Click here
Q99KR3 View 3D Structure Click here
Q9C8L4 View 3D Structure Click here
Q9C952 View 3D Structure Click here
Q9DB32 View 3D Structure Click here
Q9DCM0 View 3D Structure Click here
Q9H777 View 3D Structure Click here
Q9QXK7 View 3D Structure Click here
Q9SID3 View 3D Structure Click here
Q9UKF6 View 3D Structure Click here
Q9UT36 View 3D Structure Click here
Q9VLS9 View 3D Structure Click here
Q9VMI8 View 3D Structure Click here
Q9XXJ1 View 3D Structure Click here