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16  structures 2238  species 1  interaction 3875  sequences 16  architectures

Family: YceI (PF04264)

Summary: YceI-like domain

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This is the Wikipedia entry entitled "YceI protein domain". More...

YceI protein domain Edit Wikipedia article

YceI
PDB 1wub EBI.jpg
Crystal structure of the polyisoprenoid-binding protein, TT1927B, from Thermus thermophilus hb8
Identifiers
Symbol YceI
Pfam PF04264
InterPro IPR007372
SCOP 1uf6
SUPERFAMILY 1uf6

In molecular biology, Yce-I protein domain is a putative periplasmic protein. This entry represents the lipid-binding protein YceI from Escherichia coli [1] and the polyisoprenoid-binding protein TTHA0802 from Thermus thermophilus.[2] Its role is to help aid the biosynthesis of isoprenoid, an important molecule found in all living organisms.

Structure[edit]

Both of these proteins share a common domain with an 8-stranded beta-barrel fold. This resembles the lipocalin fold, although no sequence homology exists with lipocalins. In TTHA0802, the protein binds the polyisoprenoid chain within the pore of the barrel via hydrophobic interactions.[2] Sequence homologues of this core structure are present in a wide range of bacteria and archaea.

Function[edit]

The crystal structures suggests that this family of proteins plays an important role in isoprenoid quinone metabolism or in transport or storage. In both cases, the protein is a homodimer, each monomer being characterized by a lipocalin fold.[2]

References[edit]

  1. ^ Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL (August 2002). "pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli". J. Bacteriol. 184 (15): 4246–58. PMC 135203. PMID 12107143. 
  2. ^ a b c Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S (April 2005). "Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8". Protein Sci. 14 (4): 1004–10. doi:10.1110/ps.041183305. PMC 2253440. PMID 15741337. 

This article incorporates text from the public domain Pfam and InterPro IPR007372

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.

YceI-like domain Provide feedback

E. coli YceI is a base-induced periplasmic protein [1]. The recent structure of a member of this family shows that it binds to polyisoprenoid [2]. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold.

Literature references

  1. Stancik LM, Stancik DM, Schmidt B, Barnhart DM, Yoncheva YN, Slonczewski JL; , J Bacteriol 2002;184:4246-4258.: pH-Dependent Expression of Periplasmic Proteins and Amino Acid Catabolism in Escherichia coli. PUBMED:12107143 EPMC:12107143

  2. Handa N, Terada T, Doi-Katayama Y, Hirota H, Tame JR, Park SY, Kuramitsu S, Shirouzu M, Yokoyama S; , Protein Sci. 2005;14:1004-1010.: Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8. PUBMED:15741337 EPMC:15741337


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007372

This entry represents the lipid-binding protein YceI from Escherichia coli [PUBMED:12107143] and the polyisoprenoid-binding protein TTHA0802 from Thermus thermophilus [PUBMED:15741337]. Both these proteins share a common domain with an 8-stranded beta-barrel fold, which resembles the lipocalin fold, although no sequence homology exists with lipocalins. In TTHA0802, the protein binds the polyisoprenoid chain within the pore of the barrel via hydrophobic interactions [PUBMED:15741337]. Sequence homologues of this core structure are present in a wide range of bacteria and archaea. The crystal structures of Yce1 and TTHA0802 suggest that this family of proteins plays an important role in isoprenoid quinone metabolism and/or transport and/or storage [PUBMED:15741337].

Domain organisation

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

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Alignments

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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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(135)
Full
(3875)
Representative proteomes NCBI
(2995)
Meta
(1071)
RP15
(378)
RP35
(777)
RP55
(993)
RP75
(1127)
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Format an alignment

  Seed
(135)
Full
(3875)
Representative proteomes NCBI
(2995)
Meta
(1071)
RP15
(378)
RP35
(777)
RP55
(993)
RP75
(1127)
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
(135)
Full
(3875)
Representative proteomes NCBI
(2995)
Meta
(1071)
RP15
(378)
RP35
(777)
RP55
(993)
RP75
(1127)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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.

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:

HMM logo

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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: COG2353
Previous IDs: none
Type: Domain
Author: Kerrison ND, Finn RD, Bateman A
Number in seed: 135
Number in full: 3875
Average length of the domain: 164.90 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 82.66 %

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 20.5 20.5
Trusted cut-off 21.0 21.0
Noise cut-off 20.3 18.6
Model length: 164
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Interactions

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

YceI

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 YceI 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 seqence.

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