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
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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)
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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.
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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:
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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.
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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:
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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.
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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:
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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.
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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.
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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).
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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:
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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:
- X-ray crystallography (293 K; pH: 5.6; PEG 4000)
| References:
- 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.
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References |
- 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
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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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