Detailed information NTG0001028

Experimentally validated

Overview

• Name: pilF
• Type: Machinery gene
• Locus tag: TT_RS08215
• Genome accession: NC_005835
• Coordinates: 1541858..1544527 (-)
• Length: 889 a.a.
• NCBI ID: WP_011173991.1
• Uniprot ID: Q72H73
• Organism: Thermus thermophilus HB27
• Function: power the assembly of type IV pilus DNA binding and uptake

Function

The assembly of the DNA transporter pseudopilus in T. thermophilus is powered by the unique polymerization ATPase PilF, which binds two second messenger c-di-GMP molecules. PilF was found to be connected to the pseudopilus in T. thermophilus via PilM as coupling protein.

Genomic Context

Location: 1536858..1549527

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
TT_RS08195 (TT_C1618)	-	1537704..1538336 (-)	633	WP_011173987.1	histidine phosphatase family protein	-
TT_RS08200 (TT_C1619)	purM	1538333..1539334 (-)	1002	WP_011173988.1	phosphoribosylformylglycinamidine cyclo-ligase	-
TT_RS08205 (TT_C1620)	gatB	1539340..1540749 (-)	1410	WP_011173989.1	Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB	-
TT_RS08210 (TT_C1621)	pilT	1540760..1541845 (-)	1086	WP_011173990.1	type IV pilus twitching motility protein PilT	Machinery gene
TT_RS08215 (TT_C1622)	pilF	1541858..1544527 (-)	2670	WP_011173991.1	type IV pilus assembly ATPase PilB	Machinery gene
TT_RS08220 (TT_C1623)	-	1544524..1545009 (-)	486	WP_011173992.1	YqeG family HAD IIIA-type phosphatase	-
TT_RS08225 (TT_C1624)	pgeF	1545044..1545772 (-)	729	WP_011173993.1	peptidoglycan editing factor PgeF	-
TT_RS08230 (TT_C1625)	surE	1545769..1546524 (-)	756	WP_011173994.1	5'/3'-nucleotidase SurE	-
TT_RS08235 (TT_C1626)	-	1546583..1546789 (-)	207	WP_011173995.1	cold-shock protein	-
TT_RS08240 (TT_C1627)	-	1546947..1548236 (+)	1290	WP_011173996.1	ABC transporter substrate-binding protein	-
TT_RS08245 (TT_C1628)	-	1548288..1549163 (+)	876	WP_011173997.1	carbohydrate ABC transporter permease	-

Sequence

Protein

• Length: 889 a.a.
• Molecular weight: 98213.34 Da
• Isoelectric Point: 5.3348

>NTDB_id=1028 TT_RS08215 WP_011173991.1 1541858..1544527(-) (pilF) [Thermus thermophilus HB27]
MSVLTIGDKRLGAALLDAGLLTDEELQRALERHREVGGSLAEVLVDMGLLSERRIAQTIEDRFGIPLVELHRVEIPPKVK
ALLPAEKAKELKAIPFALDEEAGVVRVAFLNPLDTLSLEEVEDLTGLVVEPYQTTKSAFLYALAKHYPELGLPVPPPPSG
EGQKDLKLGELLLQKGWISREALEEALVEQEKTGDLLGRILVRKGLPEEALYRALAEQKGLEFLESTEGIVPDPSAALLL
LRSDALRYGAVPIGFQNGEVEVVLSDPRHKEAVAQLLNRPARFYLALPQAWEELFRRAYPQKNRLGEVLVQEGKLSREAL
KEALEVQKGLPRAKPLGEILVELGLARPEDVEEALQKQRRGGGRLEDTLVQSGKLRPEALAQAVATQLGYPYVDPEEDPP
DPGAPLLLPEDLCRRYGVFPHRLEGNRLVLLMKDPRNILALDDVRLALKRKGLNYEVAPAVATEAAITKLIERFYGKAEL
SEIAKEFAKKQAEEEVPSPLELDESAAQKFVKQVIREAFLQDASDIHIEPRQNDVQVRLRIDGALRPYSTLPKGALNAVI
SVVKIMGGLNIAEKRLPQDGRVRYREGAIDVDLRLSTLPTVYGEKAVMRLLKKASDIPEIEDLGFAPGVFERFKEVISKP
YGIFLITGPTGSGKSFTTFSILKRIATPDKNTQTIEDPVEYEIPGINQTQVNPQAGLTFARALRAFLRQDPDIIMVGEIR
DSETAKIATEAALTGHLVIATLHTNDAAQAITRLDEMGVEPFNISAALIGVLSQRLVRRVCEHCKVEVKPDPETLRRLGL
SEAEIQGARLYKGMGCERCGGTGYKGRYAIHELLVVDDEIRHAIVAGKSATEIKEIARRKGMKTLREDGLYKALQGITTL
EEVLARTIE

Nucleotide

• Length: 2670 bp

>NTDB_id=1028 TT_RS08215 WP_011173991.1 1541858..1544527(-) (pilF) [Thermus thermophilus HB27]
ATGAGCGTGCTCACCATAGGGGACAAAAGGCTCGGGGCGGCCCTCTTGGACGCCGGGCTCCTCACGGACGAGGAGCTGCA
GCGGGCCTTGGAACGGCACCGGGAGGTGGGGGGCTCCTTGGCCGAGGTCCTGGTGGACATGGGCCTCCTCTCCGAGAGGA
GGATCGCCCAGACCATTGAGGACCGCTTCGGCATCCCCCTGGTGGAGCTCCACCGGGTGGAGATCCCCCCCAAGGTCAAG
GCCCTCCTTCCCGCGGAGAAGGCCAAGGAACTCAAGGCCATCCCCTTCGCCCTGGACGAGGAGGCGGGGGTGGTGCGGGT
GGCCTTCCTCAACCCCCTGGACACCCTGAGCCTCGAGGAGGTGGAGGACCTCACGGGGCTCGTGGTGGAGCCGTACCAGA
CCACCAAAAGCGCCTTCCTCTACGCCCTGGCCAAACACTACCCGGAGCTCGGCCTTCCCGTCCCCCCGCCGCCTTCGGGC
GAGGGCCAGAAGGACCTCAAGCTCGGGGAGCTCCTCCTGCAAAAGGGGTGGATCTCCCGCGAGGCCCTGGAGGAGGCCTT
GGTGGAACAGGAGAAGACGGGGGACCTCCTCGGGCGGATCCTGGTGCGGAAGGGGCTCCCCGAGGAGGCCCTTTACCGGG
CCTTGGCGGAGCAGAAGGGGCTGGAGTTTCTGGAAAGCACCGAGGGGATCGTCCCCGACCCCTCCGCCGCCCTCCTCCTC
CTCCGCTCCGACGCCCTGCGTTACGGCGCCGTGCCCATCGGCTTCCAAAACGGGGAGGTGGAGGTGGTCCTCTCCGACCC
CCGGCACAAGGAGGCGGTGGCCCAGCTCCTCAATCGGCCCGCCCGCTTCTACCTCGCCCTCCCCCAGGCCTGGGAGGAGC
TCTTCCGCCGGGCCTACCCGCAGAAGAACCGCCTGGGGGAGGTCCTGGTCCAGGAGGGCAAGCTCTCCCGGGAAGCGCTG
AAGGAGGCCCTGGAGGTGCAGAAAGGCCTGCCCCGGGCCAAGCCTTTGGGGGAGATCCTGGTGGAGCTCGGCCTCGCCCG
CCCCGAGGACGTGGAGGAGGCCCTGCAGAAGCAAAGGCGGGGCGGGGGCCGGCTGGAGGACACCCTGGTCCAGTCGGGGA
AGCTCAGGCCCGAGGCCCTGGCCCAGGCGGTGGCCACCCAGCTGGGCTACCCCTACGTTGACCCCGAGGAGGACCCCCCC
GATCCCGGCGCCCCCCTCCTCCTCCCAGAGGACCTGTGCCGCCGCTATGGGGTCTTCCCCCACCGCCTCGAGGGAAACCG
CCTCGTCCTCCTGATGAAGGACCCGAGGAACATCCTGGCCCTGGACGACGTGCGCCTCGCCCTCAAGAGGAAGGGCCTGA
ACTACGAAGTGGCCCCCGCCGTGGCCACGGAGGCCGCCATCACCAAGCTCATCGAGCGCTTCTACGGCAAGGCCGAGCTC
TCGGAGATCGCCAAGGAGTTCGCCAAAAAGCAGGCGGAGGAGGAGGTCCCAAGCCCCCTGGAGCTGGACGAGAGCGCCGC
CCAGAAGTTCGTGAAGCAGGTGATCCGGGAGGCCTTCCTCCAGGACGCCTCCGACATCCACATTGAGCCCAGGCAGAACG
ACGTCCAGGTGCGCCTCCGGATTGACGGCGCCCTGCGGCCGTACAGCACCCTGCCCAAGGGGGCGCTGAACGCGGTGATC
TCCGTGGTCAAGATCATGGGCGGGCTCAACATCGCCGAGAAGCGCCTCCCCCAGGACGGACGGGTGCGCTACCGGGAAGG
GGCCATAGACGTGGACCTCCGGCTTTCCACCCTGCCCACGGTCTACGGGGAGAAGGCGGTGATGCGCCTCCTCAAGAAGG
CCTCGGACATCCCCGAGATCGAGGACCTGGGCTTCGCCCCGGGGGTGTTTGAACGCTTCAAGGAGGTGATCTCCAAGCCC
TACGGCATCTTCCTCATCACCGGGCCCACGGGGTCGGGCAAGAGCTTCACCACCTTCTCCATCCTCAAGCGCATCGCCAC
CCCCGACAAGAACACCCAGACCATTGAAGACCCCGTGGAGTACGAGATCCCCGGGATCAACCAGACCCAGGTGAACCCCC
AGGCGGGCCTCACCTTCGCCCGGGCGCTAAGGGCCTTCCTCAGGCAGGACCCGGACATCATCATGGTGGGGGAGATCCGG
GACTCCGAGACGGCCAAGATCGCCACCGAAGCCGCCCTCACCGGCCACCTCGTCATCGCCACCCTGCACACCAACGACGC
CGCCCAGGCCATCACCCGCCTGGACGAGATGGGGGTGGAGCCCTTCAACATCTCCGCGGCCCTCATCGGCGTCCTCTCCC
AGCGCCTGGTGCGCAGGGTGTGCGAGCACTGCAAGGTGGAGGTCAAGCCGGACCCCGAGACCCTCAGGCGCCTCGGGCTT
TCCGAGGCGGAGATCCAAGGGGCCAGGCTCTACAAGGGCATGGGGTGCGAGCGGTGCGGCGGCACCGGGTACAAGGGCCG
CTACGCCATCCACGAGCTTTTGGTGGTGGACGACGAGATCCGCCACGCCATCGTGGCGGGGAAGTCGGCCACGGAGATCA
AGGAGATCGCCCGGAGGAAGGGGATGAAGACCCTGAGGGAGGACGGCCTCTACAAGGCCCTCCAAGGGATCACCACCCTC
GAGGAGGTCCTGGCGCGTACCATTGAGTAA

Domains

Predicted by InterproScan.

• Type II/IV secretion system protein (T2SSE) (513-779)

• Type II secretion system (T2SS), protein E, N-terminal domain (MshEN) (369-479)

• Type II secretion system (T2SS), protein E, N-terminal domain (MshEN) (201-302)

• Type II secretion system (T2SS), protein E, N-terminal domain (MshEN) (44-148)

3D structure

• PDB: 8PKZ

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
pilB	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	56.229	100	0.565
pilB	Vibrio cholerae strain A1552	40.111	96.263	0.386
pilB	Haemophilus influenzae 86-028NP	36.134	100	0.371
pilB	Haemophilus influenzae Rd KW20	36.134	100	0.371
pilB	Vibrio campbellii strain DS40M4	36.833	100	0.369
pilB	Vibrio parahaemolyticus RIMD 2210633	36.396	100	0.367
pilB	Acinetobacter baumannii D1279779	37.011	98.596	0.365
pilB	Legionella pneumophila strain ERS1305867	38.848	93.728	0.364
pilB	Glaesserella parasuis strain SC1401	35.01	100	0.362

References

• [1]: Konstantin Neißner et al. (2025) The structural basis for high-affinity c-di-GMP binding to the GSPII-B domain of the traffic ATPase PilF from Thermus thermophilus. The Journal of Biological Chemistry 301(1):108041. [PMID: 39615687]
• [2]: Konstantin Neißner et al. (2025) NMR Solution Structure of the N-Terminal GSPII Domain from the Thermus Thermophilus Traffic ATPase PilF and Reconstruction of its c-di-GMP Binding Capability. Chembiochem : A European Journal of Chemical Biology 26(7):e202400959. [PMID: 39960869]
• [3]: Beate Averhoff et al. (2021) Natural transformation in Gram-negative bacteria thriving in extreme environments: from genes and genomes to proteins, structures and regulation. Extremophiles : Life Under Extreme Conditions 25(5-6):425-436. [PMID: 34542714]
• [4]: Kerstin Kruse et al. (2019) The traffic ATPase PilF interacts with the inner membrane platform of the DNA translocator and type IV pili from Thermus thermophilus. FEBS Open Bio 9(1):4-17. [PMID: 30652069]
• [5]: Kerstin Kruse et al. (2018) Functional dissection of the three N-terminal general secretory pathway domains and the Walker motifs of the traffic ATPase PilF from Thermus thermophilus. Extremophiles : Life Under Extreme Conditions 22(3):461-471. [PMID: 29464394]
• [6]: Ralf Salzer et al. (2014) Type IV pilus biogenesis, twitching motility, and DNA uptake in Thermus thermophilus: discrete roles of antagonistic ATPases PilF, PilT1, and PilT2. Applied And Environmental Microbiology 80(2):644-52. [PMID: 24212586]
• [7]: Ralf Salzer et al. (2014) Zinc and ATP binding of the hexameric AAA-ATPase PilF from Thermus thermophilus: role in complex stability, piliation, adhesion, twitching motility, and natural transformation. The Journal of Biological Chemistry 289(44):30343-30354. [PMID: 25202014]
• [8]: Richard F Collins et al. (2013) Structure and mechanism of the PilF DNA transformation ATPase from Thermus thermophilus. The Biochemical Journal 450(2):417-25. [PMID: 23252471]
• [9]: Ralf Salzer et al. (2013) The DNA uptake ATPase PilF of Thermus thermophilus: a reexamination of the zinc content. Extremophiles : Life Under Extreme Conditions 17(4):697-8. [PMID: 23712905]
• [10]: Ilona Rose et al. (2011) Identification and characterization of a unique, zinc-containing transport ATPase essential for natural transformation in Thermus thermophilus HB27. Extremophiles : Life Under Extreme Conditions 15(2):191-202. [PMID: 21210168]
• [11]: Cornelia Schwarzenlander et al. (2009) The role of single subunits of the DNA transport machinery of Thermus thermophilus HB27 in DNA binding and transport. Environmental Microbiology 11(4):801-8. [PMID: 19396940]
• [12]: Alexandra Friedrich et al. (2002) Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Applied And Environmental Microbiology 68(2):745-55. [PMID: 11823215]