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   TM1081;TM1081
Protein Sequence Comparative Analysis   (PSCA)
 
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TM1081    TM1081            JCSG 282948 PDB Deposition 08-OCT-31              PDB id: 2ka5, 3f43

Protein Sequence Information


TOPSAN
JCSG Internal annotations

ACCESSIONTM1081
DESCRIPTIONPutative anti-sigma factor antagonist TM1081 [SpoIIaa-like]
ORGANISMThermotoga maritima
COMMENT282948 from Thermotoga maritima encodes a small protein (113 aa), which belongs to the anti-
sigma-factor antagonist family and has sequence similarity to the STAS (after Sulphate Transporter and
AntiSigma factor antagonist) family (PF01740) from Pfam. By similarity, it is speculated that in the
phosphorylated form on a serine residue, the protein could act as an anti-anti-sigma factor that
counteracts an anti-sigma factor and thus release a sigma factor from inhibition. The phosphorylation
site (Ser 55) is shown as dots in the below figure.
The protein is structurally similar as many other anti sigma F factors. They include the several
structures of the Bacillus Anti-sigma factor SpoIIAB in complex with the Anti-anti-sigma SpoIIAA (see
refernce #1, PDB codes:1th8, 1thn, 1tid, and 1til, which has a rmsd 1.5A for 110 aligned Ca, 25% seq
id), the TM1442 protein from Thermotoga maritima (see refernce #2, PDB code: 1vc1, rmsd 1.7A for
105 aligned Ca, 36% seq id), the anti-sigma factor antagonist SPOIIAA in its unphosphorylated form
(see refernce #3, PDB code: 1h4y and 1h4x (rmsd 1.7A for 108 aligned Ca, 19% seq id). The
superposition of 282948 with the above structures are shown as below. 282948 (green), 1h4x(yellow),
1th8 (orange) and 1vc1 (grey). All of the similar structures are in the anti-sigma factor antagonist
SPOIIAA family from SCOP.
The interface calculation suggests that biomolecule of 282948 is a dimer.
References:

1. Masuda, S., Murakami, K.S., Wang, S., Olson, C.A., Donigian, J., Leon, F., Darst, S.A., Campbell,
E.A. (2004) Crystal Structures of the ADP and ATP Bound Forms of the Bacillus Anti-sigma Factor
SpoIIAB in Complex with the Anti-anti-sigma SpoIIAA. J.Mol.Biol. 340: 941-956
2. Lee, J.Y., Ahn, H.J., Ha, K.S., Suh, S.W. (2004) Crystal structure of the TM1442 protein from
Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma
factor RsbV Proteins 56: 176-179
3. Seavers, P.R., Lewis, R.J., Brannigan, J.A., Verschueren, K.H., Murshudov, G.N., Wilkinson, A.J.
(2001) Structure of the Bacillus cell fate determinant SpoIIAA in phosphorylated and unphosphorylated
forms. Structure 9: 605-614


-!- FUNCTION: IN THE PHOSPHORYLATED FORM IT COULD ACT AS AN ANTI-ANTI-
SIGMA FACTOR THAT COUNTERACTS AN ANTI-SIGMA FACTOR AND THUS
RELEASE A SIGMA FACTOR FROM INHIBITION (BY SIMILARITY).
-!- PTM: PHOSPHORYLATED ON A SERINE RESIDUE (BY SIMILARITY).
-!- SIMILARITY: BELONGS TO THE ANTI-SIGMA-FACTOR ANTAGONIST FAMILY.
-!- SIMILARITY: CONTAINS 1 STAS DOMAIN.
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DR UNIPROT; Y1081_THEMA
DR SPTR; Q9X0H0 (flat text); Q9X0H0 (good view)
DR GenBank; AAD36158
DR Pfam; PF01740; STAS;
DR Interpro; IPR003658; Antisig_antgnst;
DR Interpro; IPR002645; STAS;
DR PDB; 2KA5; Identical; 25-NOV-08; PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM_1081;
DR PDB; 3F43; Identical; 25-NOV-08; PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM1081;
DR PDB; 1VC1; Highly similar; 28-SEP-04; PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM1442;
DR PDB; 1SBO; Highly similar; 21-DEC-04; PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM1442;
DR PDB; 1T6R; Highly similar; 24-MAY-05; PUTATIVE ANTI-SIGMA FACTOR ANTAGONIST TM1442;
DR FFAS; 282948; Fold and function assignment.
DR TVPC; TM1081; Homologs in PDB, JCSG and SG center.
DR OVP; TM1081; Ortholog view popup.
DR TPM; TM1081; Target PDB monitor.
DR FSS; TM1081; Target function coverage.
PROPERTY Residues: 113 aa
Molecule Weight: 12972.43 Dalton
Isoelectric Point: 5.4
Extinction Coefficient: 9970
Gravy Index: .14
Number of Met residues: 3
Percentage of Met residues: 2.65 %
Number of Cys residues: 0
Percentage of Cys residues: 0.00 %
SEQUENCE  amino acids 113 aa
>TM1081  TM1081 anti-sigma factor antagonist, putative
MFPYKIVDDVVILMPNKELNIENAHLFKKWVFDEFLNKGYNKIFLVLSDVESIDSFSLGV
IVNILKSISSSGGFFALVSPNEKVERVLSLTNLDRIVKIYDTISEAMEEVRRK

CDS  cDNA 339 bp
   1 atgtttccct acaagattgt ggatgacgtg gtgatactga tgccgaacaa agagctcaac    60
  61 atagagaacg cgcatctgtt caaaaaatgg gtttttgacg agtttttgaa caagggttac   120
 121 aacaagatat ttctggtcct ctcggatgtg gagagcatag acagcttcag tctgggtgtc   180
 181 attgtaaaca tcttgaagag tatcagcagc agtggtggtt tctttgcact ggtgtctcca   240
 241 aacgagaagg tagagcgagt cctttctctg acgaatctgg atcgcatagt gaagatatac   300
 301 gatacgatat cggaggccat ggaggaggtg cgaagaaag   339
Target constructs
Download sequence in PIR or FASTA format
Chemical properties of sequence with tag
GENE PREDICTION
LEFT END RIGHT END FRAME PREDICTOR SCORE 
1096565 1096906 -2 Glimmer3 score 11.81 poor
Genemark probabilities .81   .99 good
GenemarkHMM class 1 good

Notes

The start codon is a ATG/Methionine in most of sequences, but the GTG/V, TTG/L, CTG/I can be the start codons in some cases as expressing in E.coli. The start codon warning is labelled by RED color in sequence(sample: 10174951).

Protein sequence information contains the annotation contents from both of JCSG and SWISS-PROT. The SWISS-PROT/TrEMBL annotation is accessed from SWALL(SPTR) on the EBI SRS server. PDB homologes show both identical and highly similar proteins with released date and protein function.


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