This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity.
>PRK04015 DNA/RNA-binding protein albA; Provisional
>PF01918 Alba: Alba; InterPro: IPR002775 Members of this family include the archaeal protein Alba and a number of eukaryotic proteins with no known function
The DNA/RNA-binding protein Alba binds double-stranded DNA tightly but without sequence specificity. It binds rRNA and mRNA in vivo, and may play a role in maintaining the structural and functional stability of RNA, and, perhaps, ribosomes. It is distributed uniformly and abundantly on the chromosome. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner []. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenance of chromatin architecture and thereby in transcription repression. For further information see [].; GO: 0003676 nucleic acid binding; PDB: 3TOE_B 3IAB_A 1NFJ_A 1NFH_B 2Q3V_B 1VM0_B 1NH9_A 1Y9X_A 3U6Y_C 2H9U_A ....
>KOG2567 consensus Uncharacterized conserved protein [Function unknown]
2.1.1 from EC (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources [, ] show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Pichia angusta (Yeast) (Hansenula polymorpha), there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) 2.2.1.3 from EC (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 1-deoxyxylulose-5-phosphate synthase (DXP synthase) [] is an enzyme so far found in bacteria (gene dxs) and plants (gene CLA1) which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D- xylulose-5-phosphate (dxp), a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). DXP synthase is evolutionary related to TK. The N-terminal section, contains a histidine residue which appears to function in proton transfer during catalysis []. In the central section there are conserved acidic residues that are part of the active cleft and may participate in substrate-binding []. This family includes transketolase enzymes 2.2.1.1 from EC and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit P37941 from SWISSPROT 1.2.4.4 from EC. Both these enzymes utilise thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1NGS_B 1TKA_A 1TRK_B 1TKB_A 1GPU_B 1AY0_B 1TKC_B 2E6K_A 3JU3_A 2R8P_B ....
>2bky_A DNA/RNA-binding protein ALBA 1; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 1h0x_A* 1h0y_A* 1y9x_A
>2h9u_A DNA/RNA-binding protein ALBA 2; archaea, DNA binding protein, structural G NPPSFA, national project on protein structural and function analyses; 2.00A {Aeropyrum pernix} PDB: 3u6y_A*
>2bky_X DNA/RNA-binding protein ALBA 2; archaeal DNA binding protein, DNA condensation, DNA-binding, DNA binding protein; 1.70A {Sulfolobus solfataricus} SCOP: d.68.6.1 PDB: 2a2y_A 1udv_A
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Methanococcus jannaschii [TaxId: 2190]
Score = 54.7 bits (132), Expect = 5e-12
Identities = 17/69 (24%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 14 RYMQQHNEVELSALGMAIATVVTIAEILKN---NGLAVEKKITTSTVDIREETGGRPVQK 70
+ ++EV + A G AI V +AE+++N + ++K + + V
Sbjct: 21 TQLTSNDEVIIKARGKAINKAVDVAEMIRNRFIKDIKIKKIEIGTDKVKNPDGREVNV-- 78
Query: 71 AKIEILLGK 79
+ IEI+L K
Sbjct: 79 STIEIVLAK 87
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
Score = 47.8 bits (114), Expect = 2e-09
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 17 QQHNEVELSALGMAIATVVTIAEILKN---NGLAVEKKITTSTVDIREETGGRPVQKAKI 73
+ +EV + A G AI+ V +AEI++N G+ V++ + E+ V + I
Sbjct: 24 EGADEVVIKARGRAISRAVDVAEIVRNRFMPGVKVKEIKIDTEELESEQGRRSNV--STI 81
Query: 74 EILLGK 79
EI+L K
Sbjct: 82 EIVLAK 87
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]
Score = 35.1 bits (81), Expect = 2e-04
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 17 QQHNEVELSALGMAIATVVTIAEILKNNGLAVE---KKITTSTVDIREETGGRPVQKAKI 73
Q +E+ + A G AI+ V EI++N L + K+I + + + GR + + I
Sbjct: 24 QGVSEIVIKARGRAISKAVDTVEIVRNRFLPDKIEIKEIRVGSQVVTSQ-DGRQSRVSTI 82
Query: 74 EILLGK 79
EI + K
Sbjct: 83 EIAIRK 88
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287]
Score = 33.2 bits (76), Expect = 0.001
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 17 QQHNEVELSALGMAIATVVTIAEILKNNGLAVEKKITTSTVDIREETGGRPVQKAKIEIL 76
Q +EV L G I+ V + LK+ + + V E + + I +
Sbjct: 26 QGIDEVILKGTGREISKAVDVYNSLKDR---LGDGVQLVNVQTGSE-VRDRRRISYILLR 81
Query: 77 LGK 79
L +
Sbjct: 82 LKR 84
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Methanococcus jannaschii [TaxId: 2190]
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b1 [TaxId: 2287]
class: Alpha and beta proteins (a+b)
fold: IF3-like
superfamily: AlbA-like
family: DNA-binding protein AlbA
domain: DNA-binding protein AlbA
species: Archaeon Sulfolobus solfataricus, Sso10b2 [TaxId: 2287]
