Detailed information    

experimental Experimentally validated

Overview

Name   pilD   Type   Machinery gene
Locus tag   DR_RS10600 Genome accession   NC_001263
Coordinates   2079839..2081005 (+) Length   388 a.a.
NCBI ID   WP_010888696.1    Uniprot ID   Q9RSQ9
Organism   Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539     
Function   assembly of type IV pilus   
DNA binding and uptake

Function

We identified the factors (PilQ, PilD, type IV pilins, PilB, PilT, ComEC-ComEA, and ComF) involved in DNA uptake and DNA translocation across the external and cytoplasmic membranes and showed that the DNA-uptake machinery is similar to that described in the Gram negative bacterium Vibrio cholerae.


Genomic Context

Location: 2074839..2086005
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  DR_RS10580 (DR_2060) - 2075052..2075342 (+) 291 WP_027479958.1 hypothetical protein -
  DR_RS10585 (DR_2061) - 2075418..2075855 (+) 438 WP_034350316.1 hypothetical protein -
  DR_RS10590 (DR_2062) - 2075861..2076871 (-) 1011 WP_010888693.1 WD40 repeat domain-containing protein -
  DR_RS10595 (DR_2063) pnp 2076963..2079302 (+) 2340 WP_027479957.1 polyribonucleotide nucleotidyltransferase -
  DR_RS10600 (DR_2065) pilD 2079839..2081005 (+) 1167 WP_010888696.1 prepilin peptidase Machinery gene
  DR_RS10605 (DR_2066) - 2081207..2081665 (-) 459 WP_010888697.1 divergent PAP2 family protein -
  DR_RS10610 (DR_2067) nusB 2081689..2082267 (-) 579 WP_010888698.1 transcription antitermination factor NusB -
  DR_RS10615 (DR_2068) - 2082264..2082671 (-) 408 WP_010888699.1 Asp23/Gls24 family envelope stress response protein -
  DR_RS10620 (DR_2069) ligA 2082742..2084826 (-) 2085 WP_051618817.1 NAD-dependent DNA ligase LigA -

Sequence

Protein


Download         Length: 388 a.a.        Molecular weight: 41204.65 Da        Isoelectric Point: 5.8430

>NTDB_id=1305 DR_RS10600 WP_010888696.1 2079839..2081005(+) (pilD) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539]
MNVDTLIVLFAGLLGLLVGSFSNVLIWRLPRGENIAFPPSHCPKCDHPLKPTDLVPVFSWLALGGRCRYCRAPINPRYPV
VELLTGVAYAVIAATFPLSTYEAGTLGLMVLFTILLVGSAIDLDTMTLPDELTLPGTLLGVLFGLAGAGLYAQEGQLGLP
NVAQAVEGALMGAGVIVLISVYGSWVLRRFRERQWPEAPIGYQQISLGLLAGAWLGPWWGLGVALLSAAVNVAAKKAVRI
PELLTLGGFLVSLALSSAGTGPGLLDMLRGGLMAAGAVSLVCGVYWWIYWRRNKQAEDDGTDDEQSDPVAMGFGDVKLAA
VIGAFLGWERLLLAVVVAIFAGAVLGLVQLALKQENRVKFGPYLALGAVVALLWGGPLLDWYRGLLGM

Nucleotide


Download         Length: 1167 bp        

>NTDB_id=1305 DR_RS10600 WP_010888696.1 2079839..2081005(+) (pilD) [Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539]
GTGAACGTCGACACCCTCATCGTCCTCTTCGCCGGGCTGCTGGGCCTGCTGGTGGGGTCTTTTTCCAATGTGCTGATCTG
GCGCCTGCCGAGAGGCGAAAACATCGCTTTTCCGCCGAGCCACTGCCCCAAGTGCGACCATCCGCTCAAGCCCACCGACC
TCGTGCCGGTCTTTTCCTGGCTGGCGCTGGGAGGCCGCTGCCGCTACTGCCGCGCACCCATTAACCCGCGCTATCCGGTG
GTGGAACTGCTCACGGGCGTCGCCTACGCCGTCATTGCCGCGACGTTTCCGCTGAGCACCTACGAGGCGGGCACGCTGGG
ACTGATGGTGCTGTTCACGATTTTGCTCGTCGGCAGCGCGATTGACCTCGACACCATGACTCTCCCTGACGAGCTGACGC
TGCCCGGCACCCTGCTCGGCGTGCTGTTCGGGCTCGCGGGCGCGGGGCTCTACGCGCAGGAGGGTCAGTTGGGCCTGCCC
AACGTCGCGCAGGCGGTGGAAGGCGCGCTGATGGGCGCGGGCGTCATCGTCTTGATCAGCGTGTACGGCTCGTGGGTGCT
GCGGCGCTTCCGCGAACGGCAGTGGCCTGAAGCGCCCATCGGTTACCAGCAAATCAGCCTGGGGCTGCTGGCAGGCGCGT
GGCTGGGGCCGTGGTGGGGCCTGGGCGTCGCGCTGCTCTCGGCGGCGGTCAACGTGGCGGCGAAAAAGGCCGTGCGGATT
CCTGAACTGCTCACGCTGGGCGGCTTTCTGGTCAGCCTCGCCCTGAGCAGCGCGGGCACAGGGCCGGGCCTGCTCGACAT
GCTGCGCGGCGGCCTGATGGCGGCGGGCGCCGTCTCGCTCGTCTGCGGCGTGTACTGGTGGATCTACTGGCGGCGCAACA
AGCAGGCTGAAGACGACGGCACCGACGACGAGCAGAGTGACCCGGTGGCGATGGGCTTCGGGGACGTGAAGCTCGCCGCT
GTGATTGGCGCCTTTCTGGGCTGGGAGCGGCTGCTGCTTGCCGTGGTGGTGGCAATTTTTGCGGGCGCCGTGCTGGGGCT
GGTGCAACTCGCGCTCAAGCAGGAAAACCGGGTCAAGTTCGGCCCTTACCTCGCCCTGGGGGCCGTCGTCGCGCTGCTGT
GGGGCGGGCCGCTGCTGGACTGGTACCGGGGGCTGCTAGGGATGTAA

Domains

Predicted by InterproScan.

Type IV leader peptidase family (Peptidase_A24)

(109-229)

Type IV leader peptidase family (Peptidase_A24)

(238-347)

Bacterial Peptidase A24 N-terminal domain (A24_N_bact)

(13-96)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB Q9RSQ9

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value

References

[1] Solenne Ithurbide et al. (2020) Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins. Frontiers in Microbiology 11:1253. [PMID: 32625182]