RegulonDB

Gene
Name:	kdpD
Synonym(s):	ECK0683, EG10516, b0695, kac
Genome position(nucleotides):	721730 <-- 724414
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	57.58
External database links:

ASAP:	ABE-0002368
CGSC:	585
ECHOBASE:	EB0511
ECOLIHUB:	kdpD
OU-MICROARRAY:	b0695
STRING:	511145.b0695
COLOMBOS:	kdpD

Gene

Name:

kdpD

Synonym(s):

ECK0683, EG10516, b0695, kac

Genome position(nucleotides):

721730 <-- 724414

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

57.58

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

21 -> 230

HRGKLKVFFGACAGVGKTWAMLAEAQRLRAQGLDIVVGVVETHGRKDTAAMLEGLAVLPLKRQAYRGRHISEFDLDAALARRPALILMDELAHSNAPGSRHPKRWQDIEELLEAGIDVFTTVNVQHLESLNDVVSGVTGIQVRETVPDPFFDAADDVVLVDLPPDDLRQRLKEGKVYIAGQAERAIEHFFRKGNLIALRELALRRTADRV

30 -> 38

GACAGVGKT

Walker A-like motif

105 -> 109

LILMD

Walker B-like motif

401 -> 423

GCVVAAALCAVITLIAMQWLMAF

UniProt: Helical.

403 -> 507

VVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARY

Type

Positions

Sequence

Comment

21 -> 230

30 -> 38

GACAGVGKT

Walker A-like motif

105 -> 109

LILMD

Walker B-like motif

401 -> 423

GCVVAAALCAVITLIAMQWLMAF

UniProt: Helical.

403 -> 507

VVAAALCAVITLIAMQWLMAFDAANLVMLYLLGVVVVALFYGRWPSVVATVINVVSFDLFFIAPRGTLAVSDVQYLLTFAVMLTVGLVIGNLTAGVRYQARVARY

428 -> 444

LVMLYLLGVVVVALFYG

UniProt: Helical.

446 -> 466

WPSVVATVINVVSFDLFFIAP

UniProt: Helical.

463 -> 473

FIAPRGTLAVS

K⁺ recognition site

466 -> 466

P → A: reduction in sensitivity to external K⁺ concentration

469 -> 469

T → A: reduction in sensitivity to external K⁺ concentration

470 -> 470

L → A: reduction in sensitivity to external K⁺ concentration

472 -> 472

V → A: reduction in sensitivity to external K⁺ concentration

474 -> 474

D → Y: elevated kinase activity and reduced phosphatase actiitvity in vitro; constitutive expression of KdpFABC;

475 -> 498

VQYLLTFAVMLTVGLVIGNLTAGV

UniProt: Helical.

495 -> 495

T → S: reduced phosphatase activity in vitro; constitutive expression of KdpFABC

503 -> 503

R → Q/K: increase in phosphatase activity and a lower kinase activity in vitro compared to wild type; R → Q: does not affect K⁺ sensing but mutant is unable to respond to osmolarity

506 -> 506

R → Q/K: increase in phosphatase activity and a lower kinase activity in vitro compared to wild type; R → Q: does not affect K⁺ sensing but mutant is unable to respond to osmolarity

508 -> 508

R → Q/K: increase in phosphatase activity and a lower kinase activity in vitro compared to wild type; R → Q: does not affect K⁺ sensing but mutant is unable to respond to osmolarity

510 -> 510

Q → P: loss of phosphatase activity in vitro; constitutive expression of KdpFABC

511 -> 511

R → Q: increase in kinase activity and a loss of phosphatase activity in vitro compared to wild type; constitutive expression of kdpFABC which is independent of a stimulus for KdpD

527 -> 644

SPQDIAATSEQFIASTFHARSQVLLPDDNGKLQPLTHPQGMTPWDDAIAQWSFDKGLPAGAGTDTLPGVPYQILPLKSGEKTYGLVVVEPGNLRQLMIPEQQRLLETFTLLVANALER

642 -> 642

L → P: impaired homodimerization; loss of interaction with PtsN and KdpE

661 -> 726

EQIRNALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMAR

implicated in interaction with PtsN and KdpE

665 -> 730

NALLAALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSG

670 -> 883

ALSHDLRTPLTVLFGQAEILTLDLASEGSPHARQASEIRQHVLNTTRLVNNLLDMARIQSGGFNLKKEWLTLEEVVGSALQMLEPGLSSPINLSLPEPLTLIHVDGPLFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQT

UniProt: Histidine kinase.

673 -> 673

H → Q: loss of kinase activity in vitro

677 -> 677

T → M: loss of phosphatase activity and reduced phosphotransferase activity in vitro; constitutive expression of KdpFABC; see also |CITS: [27320909]|

682 -> 682

L → Q: strongly impaired interaction with PtsN; reduced interaction with KdpE

683 -> 683

F → S: loss of interaction with PtsN; F → L: strongly impaired interaction with PtsN

687 -> 687

E → G: loss of interaction with PtsN; impaired interaction with KpdE

689 -> 689

L → S/F: loss of interaction with PtsN; impaired interaction with KpdE

705 -> 705

S → R: strongly impaired interaction with PtsN; impaired interaction with KpdE

707 -> 707

I → T: loss of interaction with PtsN; impaired interaction with KpdE

708 -> 708

R → C: loss of interaction with PtsN

717 -> 717

L → R: loss of phosphatase activity in vitro; constitutive expression of KdpFABC

777 -> 882

LFERVLINLLENAVKYAGAQAEIGIDAHVEGENLQLDVWDNGPGLPPGQEQTIFDKFARGNKESAVPGVGLGLAICRAIVDVHGGTITAFNRPEGGACFRVTLPQQ

785 -> 785

L → P: impaired homodimerization; strong impairment of interaction with PtsN and KdpE

788 -> 788

N → D: loss of kinase activity in vitro

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.3 - posttranslational modification

3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.4 - complex regulation --> 3.1.2.4.3 - two component regulatory systems (external signal)

3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.2 - covalent modification, demodification, maturation

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0005829 - cytosol
GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane

molecular_function

GO:0005515 - protein binding
GO:0016740 - transferase activity
GO:0016772 - transferase activity, transferring phosphorus-containing groups
GO:0016301 - kinase activity
GO:0008134 - transcription factor binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0000155 - phosphorelay sensor kinase activity
GO:0004673 - protein histidine kinase activity
GO:0042803 - protein homodimerization activity

biological_process

GO:0035865 - cellular response to potassium ion
GO:0006470 - protein dephosphorylation
GO:0016310 - phosphorylation
GO:0000160 - phosphorelay signal transduction system
GO:0007165 - signal transduction
GO:0046777 - protein autophosphorylation
GO:0018106 - peptidyl-histidine phosphorylation

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_827	721772		reverse	nd	[RS-EPT-CBR]	[1]
	promoter	kdpEp3	721894		reverse	nd	[ICWHO]	[2]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_827

721772

reverse

[RS-EPT-CBR]

[1]

promoter

kdpEp3

721894

reverse

[ICWHO]

[2]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates
[ICWHO] Inferred computationally without human oversight

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

[ICWHO] Inferred computationally without human oversight

Reference(s)
[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.
[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

Reference(s)

[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

[2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78