DP00414: DnaK suppressor proteinFASTA viewXML view

General information
DisProt:DP00414
Name:DnaK suppressor protein
Synonym(s):DKSA_ECOLI
DksA
First appeared in release:Release 5.5 (11/17/2010)
UniProt:P0ABS1
UniGene: 
SwissProt: DKSA_ECOLI
TrEMBL:  
NCBI (GI): 78100039
Source organism:Escherichia coli (strain K12)
Sequence length:151
Percent disordered:43%
Homologues: 


Native sequence

        10         20         30         40         50         60
         |          |          |          |          |          |
MQEGQNRKTS SLSILAIAGV EPYQEKPGEE YMNEAQLAHF RRILEAWRNQ LRDEVDRTVT - 60
HMQDEAANFP DPVDRAAQEE EFSLELRNRD RERKLIKKIE KTLKKVEDED FGYCESCGVE - 120
IGIRRLEARP TADLCIDCKT LAEIREKQMA G



Functional narrative    

Dosage-dependent suppressor of a dnaK deletion mutation. It suppressed not only the temperature-sensitive growth but also the filamentous phenotype of the dnaK deletion strain, while the defect of lambda growth is not suppressed. (UniProt) "DksA protein is a crucial component of ppGGpp-dependent regulation of bacterial transcription." (Perederina)

Region 1: 1-6 Region 2: 7-33 Region 3: 34-34 Region 4: 35-68 Region 5: 69-70 Region 6: 71-74 Region 7: 75-109 Region 8: 110-131 Region 9: 132-134 Region 10: 135-151

Map of ordered and disordered regions







Note: 'Mouse' over a region to see the start and stop residues. Click on a region to see detailed information.


Region 1
Type:Disordered
Name:N-tail
Location:1 - 6
Length:6
Region sequence:

MQEGQN

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
 



Region 2
Type:Disordered - Molten Globule
Name:N-terminal Globular domain
Location:7 - 33
Length:27
Region sequence:

RKTSSLSILAIAGVEPYQEKPGEEYMN

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Region 2 N-terminal Globular domain portion and Region 8 C-terminal Globular domain portion together form the Globular domain (G-domain).


Region 2 N-terminal Globular domain contains an alpha-helix at aa 13-17.




Region 3
Type:Disordered - Extended
Name:linker
Location:34 - 34
Length:1
Region sequence:

E

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Function arises from the disordered state
Functional classes: Entropic chain
Functional subclasses: Flexible linkers/spacers
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
 



Region 4
Type:Ordered
Name:alpha-helix
Location:35 - 68
Length:34
Region sequence:

AQLAHFRRILEAWRNQLRDEVDRTVTHMQDEAAN

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Transactivation (transcriptional activation)
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Region 4 alpha-helix and Region 7 alpha-helix form a coiled coil.




Region 5
Type:Disordered - Extended
Name:CC linker
Location:69 - 70
Length:2
Region sequence:

FP

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Function arises from the disordered state
Functional classes: Entropic chain
Functional subclasses: Flexible linkers/spacers
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
 



Region 6
Type:Disordered w/ Residual Structure
Name:turn
Location:71 - 74
Length:4
Region sequence:

DPVD

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Region 6 contains a 3/10 helix.


Perederina et al (2004) observe "two highly conserved acidic residues" in Region 6 turn, D71 and D74, could possibly deliver these residues to the RNAP active site and "coordinate a functional Mg2+ ion," similar to GreA.




Region 7
Type:Ordered
Name:alpha-helix
Location:75 - 109
Length:35
Region sequence:

RAAQEEEFSLELRNRDRERKLIKKIEKTLKKVEDE

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Transactivation (transcriptional activation)
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Region 4 alpha-helix and Region 7 alpha-helix form a coiled coil.




Region 8
Type:Disordered - Molten Globule
Name:C-terminal Globular domain
Location:110 - 131
Length:22
Region sequence:

DFGYCESCGVEIGIRRLEARPT

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Unknown
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Region 8, the C-terminal globular domain, contains an alpha-helix at aa 123-131. Two residues, C114 and C117 interact with C135 and C138 of the C-terminal alpha-helix (Region 10) as part of a C4 zinc-finger motif.


Region 2 N-terminal Globular domain portion and Region 8 C-terminal Globular domain portion together form the Globular domain (G-domain).




Region 9
Type:Disordered - Extended
Name:linker
Location:132 - 134
Length:3
Region sequence:

ADL

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Function arises from the disordered state
Functional classes: Entropic chain
Functional subclasses: Flexible linkers/spacers
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
 



Region 10
Type:Ordered
Name:C-terminal alpha-helix
Location:135 - 151
Length:17
Region sequence:

CIDCKTLAEIREKQMAG

Modification type: Native
PDB: 1TJL:A
Structural/functional type: Relationship to function unknown
Functional classes: Unknown
Functional subclasses: Protein-protein binding
Detection methods:
  1. X-ray crystallography (293 K; pH: 5.6; PEG 4000)

References:
  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156

Comments:
Two residues of Region 10, C135 and C138, interact with C114 and C117 of Region 8 (C-terminal Globular domain) as part of a C4 zinc-finger motif.


According to Perederina et al (2004), "though the Zn2+-mediated interactions with the G-domain likely restrict the mobility of the CT helix, it retains a certain degree of freedom, as revealed by its somewhat distinct orientation among the independent DksA molecules in the crystal." Additionally, the CT helix is likely involved in increasing DskA's RNAP-binding affinity.




References

  1. Perederina A, Svetlov V, Vassylyeva MN, Tahirov TH, Yokoyama S, Artsimovitch I, Vassylyev DG. "Regulation through the secondary channel--structural framework for ppGpp-DksA synergism during transcription." Cell. 2004; 118(3): 297-309. PubMed: 15294156



Comments


Perederina et al (2004) note that DksA shares 'remarkable structural similarity' to another bacterial transcription factor, GreA, despite a nearly complete lack of sequence homology.



Sent for AV 11-15-2010 (PubMed: 15294156)


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