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16  structures 228  species 0  interactions 413  sequences 5  architectures

Family: LacY_symp (PF01306)

Summary: LacY proton/sugar symporter

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This is the Wikipedia entry entitled "Lactose permease". More...

Lactose permease Edit Wikipedia article

LacY proton/sugar symporter
2y5y.png
Crystal Structure of Lactose Permease in Complex with an Affinity Inactivator. PDB 2y5y[1]
Identifiers
SymbolLacY_symp
PfamPF01306
Pfam clanCL0015
InterProIPR022814
PROSITEPDOC00698
TCDB2.A.1
OPM superfamily15
OPM protein2cfq

Lactose permease is a membrane protein which is a member of the major facilitator superfamily. Lactose permease can be classified as a symporter, which uses the proton gradient towards the cell to transport β-galactosides such as lactose in the same direction into the cell.

The protein has twelve transmembrane alpha-helices and its molecular weight is 45,000 Daltons.[2] It exhibits an internal two-fold symmetry, relating the N-terminal six helices onto the C-terminal helices. It is encoded by the lacY gene in the lac operon.

The sugar lies in the hydrophilic core of the protein which is accessible from the periplasm.[2] On binding, a large conformational change takes place which makes the sugar binding site accessible from the cytoplasm.

Mechanism: hydronium ions from the outside of the cell binds to a carboxyl group on the enzyme that allows it to undergo a conformational change. This form of lactose permease can bind lactose from outside the cell. The enzyme then everts and lactose is transported inward.

The X-ray crystal structure was first solved in 2003 by J. Abramson et al.[3]

References

  1. ^ Chaptal V, Kwon S, Sawaya MR, Guan L, Kaback HR, Abramson J (June 2011). "Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition". Proceedings of the National Academy of Sciences of the United States of America. 108 (23): 9361–6. Bibcode:2011PNAS..108.9361C. doi:10.1073/pnas.1105687108. PMC 3111295. PMID 21593407.
  2. ^ a b Hammes GG (2005). Spectroscopy for the biological sciences. Hoboken, N.J.: Wiley-Interscience. p. 140. ISBN 9780471713449.
  3. ^ Abramson J, Smirnova I, Kasho V, Verner G, Kaback HR, Iwata S (August 2003). "Structure and mechanism of the lactose permease of Escherichia coli". Science. 301 (5633): 610–5. Bibcode:2003Sci...301..610A. doi:10.1126/science.1088196. PMID 12893935. S2CID 36908983.

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.

LacY proton/sugar symporter Provide feedback

This family is closely related to the sugar transporter family.

Literature references

  1. Marger MD, Saier MH Jr; , Trends Biochem Sci 1993;18:13-20.: A major superfamily of transmembrane facilitators that catalyse uniport, symport and antiport. PUBMED:8438231 EPMC:8438231


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000576

In bacteria there are a number of families of transport proteins, including symporters and antiporters, that mediate the intake of a variety of sugars with the concomitant uptake of hydrogen ions (proton symporters) [ PUBMED:8438231 ]. The lacY family of Escherichia coli and Klebsiella pneumoniae are proton/beta-galactoside symporters, which, like most sugar transporters, are integral membrane proteins with 12 predicted transmembrane (TM) regions. Also similar to the lacY family are the rafinose (rafB) and sucrose (cscB) permeases from E. coli [ PUBMED:1435727 ] and melibiose permease (melY) from Enterobacter cloacae [ PUBMED:9209070 ].

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 MFS (CL0015), which has the following description:

The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth [1]. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity [1]. All permeases of the MFS possess either 12 or 14 transmembrane helices [1].

The clan contains the following 26 members:

Acatn ATG22 BT1 CLN3 DUF5690 Folate_carrier FPN1 LacY_symp MFS_1 MFS_1_like MFS_2 MFS_3 MFS_4 MFS_5 MFS_Mycoplasma Nodulin-like Nuc_H_symport Nucleoside_tran OATP PTR2 PUCC Sugar_tr TLC TRI12 UNC-93 UVB_sens_prot

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
(4)
Full
(413)
Representative proteomes UniProt
(4608)
RP15
(24)
RP35
(132)
RP55
(405)
RP75
(988)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(4)
Full
(413)
Representative proteomes UniProt
(4608)
RP15
(24)
RP35
(132)
RP55
(405)
RP75
(988)
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  Seed
(4)
Full
(413)
Representative proteomes UniProt
(4608)
RP15
(24)
RP35
(132)
RP55
(405)
RP75
(988)
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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: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , Bateman A
Number in seed: 4
Number in full: 413
Average length of the domain: 367.90 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 95.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.0 24.0
Trusted cut-off 24.0 24.0
Noise cut-off 23.9 23.9
Model length: 413
Family (HMM) version: 22
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 LacY_symp domain has been found. There are 16 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
P02920 View 3D Structure Click here