Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map |  Home

Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR112 IGR113 IGR115 IGR114 IGR118 IGR111 IGR117 IGR120 IGR116 IGR119 atpD,atpH-2, - UU133 atpL, - UU136 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU139 p115, - UU140 atpD,atpH-2, - UU133 atpL, - UU136 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU139 p115, - UU140 Type: tandem, Name:  - 104 Type: tandem, Name:  - 101 Type: tandem, Name:  - 106 Type: tandem, Name:  - 102 Type: tandem, Name:  - 103 Type: tandem, Name:  - 105 atpD,atpH-2, - UU133 atpL, - UU136 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU139 p115, - UU140
* Calculated from Protein Sequence

Gene ID: UU134

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
atpD  atpH-1  

Definition:
ATP synthase delta chain

Gene Start:
176276

Gene Stop:
175737

Gene Length:
540

Molecular Weight*:
20463

pI*:
9.70

Net Charge*:
4.20

EC:
3.6.1.34  

Functional Class:
energy metabolism; ATP-proton motive force interconversion  

Pathway: pathway table
Oxidative phosphorylation

Primary Evidence:
Nagata K, Takagi E, Satoh H, Okamura H, Tamura T. 1995. Growth inhibition of Ureaplasma urealyticum by the proton pump inhibitor lansoprazole: direct attribution to inhibition by lansoprazole of urease activity and urea-induced ATP synthesis in U. urealyticum. Antimicrob Agents Chemother 39(10):2187-92. Medline: 8619564.

Smith DG, Russell WC, Ingledew WJ, Thirkell D. 1993. Hydrolysis of urea by Ureaplasma urealyticum generates a transmembrane potential with resultant ATP synthesis. J Bacteriol. 175(11):3253-8. Medline: 8501029.

Romano N, La Licata R, Russo Alesi D. 1986. Energy Production in Ureaplasma urealyticum. Pediatr Infect Dis. 5(6 Suppl):S308-12. Medline: 3797330.

Secondary Evidence:
Das A, Ljungdahl LG. 1997. Composition and primary structure of the F1F0 ATP synthase from the obligately anaerobic bacterium Clostridium thermoaceticum. J Bacteriol 179(11):3746-55. Medline: 9171425.

Rasmussen OF, Shirvan MH, Margalit H, Christiansen C, Rottem S. 1992. Nucleotide sequence, organization and characterization of the atp genes and the encoded subunits of Mycoplasma gallisepticum ATPase. Biochem J. 285(Pt 3):881-8. Medline: 1386735.

Comment:
F-type ATPases have 2 components, CF(1) - the catalytic core and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1), while CF(0) has three main subunits: A, B and C.

Function: This protein seems to be part of the stalk that links CF(0) to CF(1). It either transmits conformational changes from CF(0) into CF(1) or is implicated in proton conduction.

This gene is part of a cluster encompassing records UU128-UU138. The products of these genes are responsible for the ATP synthase complex, generation of ATP from ADP and Pi.

The complete list of predicted ATP synthases in U.u. is: UU053, UU054, UU128, UU129, UU130, UU132, UU133, UU134, UU135, UU136, UU137, and UU138.

This gene cluster is a likely candidate for the ATP synthase activity seen in conjunction with the urease present in Ureaplasma urealyticum (see UU427-UU434).

From: Molecular Biology and Pathogenicity of Mycoplasmas, Microbiology and Molecular Biology Reviews, Dec. 1998, p.1118-1119.Shmuel Razin, David Yogev, and Yehudith Naot.

The dependence of ureaplasmas on urea for growth has led to the hypothesis that intracellular urea hydrolysis and the resulting intracellular accumulation of ammonia/ammonium ions is coupled to ATP synthesis through a chemiosmotic type of mechanism. Experimental support for the generation of a transmembrane potential, with resultant ATP synthesis through the ureaplasmal F0F1-type ATPase, first provided by Romano et al. (1986, Medline: 3797330) was more recently extended and confirmed by Smith et al. (1993, Medline: 8501029) [...] It is worth mentioning at this point that the pH of the urogenital tract is usually on the acidic side of neutrality, corresponding to the pH values optimal for ureaplasma growth, maximum increase in delta P, maximum ammonia chemical potential, maximum urease activity, and maximum ATP generation.

NOTE: There are two genes encoding for proteins that show significant homology to AtpH proteins. Whether both of these proteins are needed for ATP synthase function, or if they act as a heterodimer remains to be experimentally derived. The fact that both proteins only have a partial domain according to Pfam may indicate that they act as a heterodimer within the ATP synthase complex.


Blast Summary:  PSI-Blast Search
A gapped BLAST reveals 8 significant hits, all of which are ATP synthase delta chain proteins. For example, residues 11-179 are 21% similar to ATPD_ODOSI (Odontella sinensis). The other significant hits were to ATPD_CYACA, 3603006, ATPD_STRBO, ATPD_BACFI, ATPD_SYNY3, ATPD_RHOBL and ATPD_BACME.

On the fifth iteration of PSI-BLAST the alignment reached convergance. Significant hits are seen against the ATP synthase delta chains of both prokaryotic and eukaryotic organisms. For example: residues 7-178 of UU134 are 17% similar to residues 6-176 of ATPD_BACCA.

COGS Summary:  COGS Search
The phylogenetic pattern of COG0712 is ehgpc-y-.
Cog name: ATP synthase delta subunit.
Functional class: C.
BeTs to e--pc---.
Number of proteins in this genome belonging to this COG is 2



Blocks Summary:  Blocks Search
Residues 7-19, 77-98, 137-174, 62-99 and 57-94 rank in the 99.53th percentile to Block BL00389(A,B,C,C and C respectively), described as ATP synthase delta (OSCP) subunit proteins.

Residues 61-79 rank in the 97.79th percentile to Block PD02910C, described as Transcription Protein Factor Regulation A.

ProDom Summary:  Protein Domain Search
Residues 11-176 are 25% similar to a defined domain of ATPD_ODOSI.


Paralogs:  Local Blast Search
UU134 is paralogously related to UU133, an ATP synthase delta chain; and UU029, a conserved hypothetical protein; possible tex protein. Residues 84-175 of UU134 are 32% similar to residues 4-91 of UU133. Residues 57-177 are 22% similar to residues 66-184 of UU029.

Pfam Summary:  Pfam Search
Residues 8 to 178 (E-value = 5.1e-09) place UU134 in the OSCP family which is described as ATP synthase delta (OSCP) subunit (PF00213)

Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
57  
84

PDB Hit:


Gene Protein Sequence:
MKSSLKPVEKYAYSIFEIAKEEKKLDLYKHNLETINSIIEEVPAFFEAVG
DPARDRNERKQIVIKNLEGEIDIYLISLIDLLIDVKSVKLLKKIVLKALD
FVNEALSVKKVLITTAYELTKNQIDRLLQSLKKKYVCEKIEPIVVVDKSI
IGGLSINFESQVLDNSLKTKLFNIVKKVN$

Gene Nucleotide Sequence:  Sequence Viewer
ATGAAATCTTCATTAAAACCAGTTGAAAAATACGCTTATTCAATTTTTGA
AATTGCTAAAGAAGAAAAAAAATTAGATTTATACAAACATAATTTGGAAA
CAATTAATTCTATCATTGAAGAGGTTCCAGCTTTTTTTGAAGCTGTTGGT
GATCCTGCTCGTGATCGTAATGAAAGAAAACAAATTGTGATTAAAAATCT
AGAAGGTGAGATTGATATTTATTTAATTAGTTTAATTGATCTACTAATTG
ATGTTAAATCGGTTAAACTACTTAAAAAAATAGTTTTAAAAGCTTTGGAT
TTTGTTAATGAAGCTTTAAGTGTTAAAAAAGTTTTAATAACAACTGCTTA
TGAATTAACAAAAAATCAAATTGATCGCCTTCTGCAATCTTTAAAAAAGA
AATATGTGTGTGAAAAAATAGAACCAATTGTTGTTGTTGATAAATCAATT
ATTGGAGGACTTTCAATTAATTTTGAATCGCAAGTTTTAGATAATAGTTT
AAAAACTAAATTATTTAATATTGTAAAAAAGGTAAATTAG


Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy