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33  structures 781  species 1  interaction 1601  sequences 3  architectures

Family: LamB (PF02264)

Summary: LamB porin

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This is the Wikipedia entry entitled "Maltoporin". More...

Maltoporin Edit Wikipedia article

LamB porin
PDB 2mpr EBI.jpg
Structure of maltoporin from Salmonella typhimurium.[1]
Identifiers
Symbol LamB
Pfam PF02264
InterPro IPR003192
SCOP 2mpr
SUPERFAMILY 2mpr
TCDB 1.B.3
OPM superfamily 32
OPM protein 2mpr
CDD cd01346

Maltoporins (or LamB porins) are a family of outer membrane proteins. Maltoporin forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel.[2] Maltoporin is a trimeric channel on the bacterial outer membrane. Most pores used for diffusion contain only 16 antiparallel strands, but Maltoporin has 18. The structure of Maltoporin contains long loops and short turns. The long loops are in contact with the cell exterior and the turns are in contact with the periplasm. This channel is involved in sugar transport. The sugar initially binds to the first greasy residue with van der Waals forces. The sugar continues through the channel by guided diffusion of the sugar along the greasy residues which form a "slide". Maltoporin's original name was LamB because it is a bacteriophage lambda receptor. This channel is specific because it has a binding site for maltosaccharides. The affinity of these maltosaccharides to the channel increases as the length of the chain increases.[3]

References[edit]

  1. ^ Meyer JE, Hofnung M, Schulz GE (March 1997). "Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside". J. Mol. Biol. 266 (4): 761–75. doi:10.1006/jmbi.1996.0823. PMID 9102468. 
  2. ^ Schirmer T, Rosenbusch JP, Keller TA, Wang YF (1995). "Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution". Science 267 (5197): 512–514. doi:10.1126/science.7824948. PMID 7824948. 
  3. ^ Ranquin,A. "Maltoporin: Sugar for physics and biology", Elsevier,Retrieved on 27 April 2004.

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.

LamB porin Provide feedback

Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel [1].

Literature references

  1. Schirmer T, Keller TA, Wang YF, Rosenbusch JP; , Science 1995;267:512-514.: Structural basis for sugar translocation through maltoporin channels at 3.1 A resolution [see comments] PUBMED:7824948 EPMC:7824948


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003192

Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel [PUBMED:7824948].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 MBB (CL0193), which has the following description:

This clan gathers together a large set of beta barrel membrane proteins.Although these proteins have different numbers of beta strands in the barrel they have significant sequence similarity between families.

The clan contains the following 54 members:

Ail_Lom Autotransporter Bac_surface_Ag Campylo_MOMP Channel_Tsx CopB DUF1302 DUF1597 DUF2320 DUF2490 DUF2860 DUF3078 DUF3138 DUF3187 DUF3308 DUF3374 DUF3575 DUF4289 DUF481 DUF560 Gcw_chp HP_OMP HP_OMP_2 KdgM LamB Legionella_OMP MipA OMP_b-brl OMP_b-brl_2 OMP_b-brl_3 OmpA_membrane Omptin OmpW Opacity OpcA OprB OprD OprF OstA_C PagL Phenol_MetA_deg Porin_1 Porin_2 Porin_4 Porin_O_P Porin_OmpG ShlB Surface_Ag_2 Toluene_X TonB_dep_Rec TraF_2 TSA Usher YfaZ

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.

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  Seed
(6)
Full
(1601)
Representative proteomes NCBI
(906)
Meta
(30)
RP15
(19)
RP35
(67)
RP55
(132)
RP75
(201)
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
(6)
Full
(1601)
Representative proteomes NCBI
(906)
Meta
(30)
RP15
(19)
RP35
(67)
RP55
(132)
RP75
(201)
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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.

Pfam alignments:

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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: Pfam-B_4810 (release 5.2)
Previous IDs: none
Type: Domain
Author: Bateman A, Mian N
Number in seed: 6
Number in full: 1601
Average length of the domain: 388.90 aa
Average identity of full alignment: 35 %
Average coverage of the sequence by the domain: 86.13 %

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 25.1 25.1
Trusted cut-off 25.1 25.7
Noise cut-off 24.1 24.7
Model length: 398
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

LamB

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 LamB domain has been found. There are 33 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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