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Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap IGR112 IGR113 IGR115 IGR114 IGR118 IGR111 IGR117 IGR116 IGR110 IGR119 atpD,atpH-2, - UU133 UU127 atpL, - UU136 atpE, - UU128 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU139 atpD,atpH-2, - UU133 UU127 atpL, - UU136 atpE, - UU128 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU139 Type: tandem, Name:  - 102 Type: tandem, Name:  - 99 Type: tandem, Name:  - 100 Type: tandem, Name:  - 101 Type: tandem, Name:  - 103 atpD,atpH-2, - UU133 atpL, - UU136 atpE, - UU128 atpI, - UU138 atpD,atpH-1, - UU134 atpF, - UU135 UU131 atp6, - UU137 atpG, - UU130 atpB, - UU129 atpA, - UU132 UU127 UU139
* Calculated from Protein Sequence

Gene ID: UU132

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
atpA  

Definition:
ATP synthase alpha chain

Gene Start:
175425

Gene Stop:
173026

Gene Length:
2400

Molecular Weight*:
89441

pI*:
4.70

Net Charge*:
-36.97

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:
The sequences of subunits alpha and beta are related (hence the paralogous relationship) and both contain a nucleotide-binding site for ATP and ADP (motif analysis reveals an ATP-GTP binding site at residues 170-177). The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Motif analysis (URL: www.motif.genome.ad.jp) also revealed a ATPASE_ALPHA_BETA signature at residues 356-365, described as a ATP synthase alpha and beta subunits signature.

Function: Produces ATP from ADP in the presence of a proton gradient across the membrane. 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) and Epsilon(1). CF(0) has three main subunits: A, B and C.

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: The last ~300 amino acids of this protein show no similarity to other AtpA proteins (in whole or in part), or any other proteins in the GenBank non-redundant database. Whether this part of the protein lends itself to a special function in Uu or is the result of an assembly or sequence error remains to be elucidated.


Blast Summary:  PSI-Blast Search
A gapped BLAST reveals significant hits to a number of ATP Synthase Alpha Chain proteins. For example: Residues 13-501 are 65% similar to the ATP synthase alpha chain of M.gallisepticum (ATPA_MYCGA). Similarly, residues 4-506 are 61% similar to the ATP synthase alpha chain of M.genitalium (ATPA_MYCGE). Other significant hits are to (but are not limited to) the ATP synthase alpha chain proteins of M.pneumoniae (ATPA_MYCPN), B.subtilis (ATPA_BACSU), and H.pylori (ATPA_HELPY).

NOTE: All similarity in the gapped BLAST results took place in approximately the first 500 amino acid residues. The remaining 300 amino acids did not show any similarity to other proteins. The contribution of these remaining 300 amino acids to protein function is unknown.

COGS Summary:  COGS Search
The phylogenetic pattern of COG0056 is ehgpc-yu.
Cog name: ATP synthase alpha subunit.
Functional class: C.
BeTs to -hg-c-yu.
Number of proteins in this genome belonging to this COG is 2



Blocks Summary:  Blocks Search
Residues 92-117, 149-186, 241-252, 260-304, 312-349 and 402-411 rank in the 100.00th percentile to Block BL00152(A,B,C,D,E and F respectively), described as ATP synthase alpha and beta subunit proteins.

Residues 165-180 rank inthe 96.94th percentile to Block PR00819B, described as CBXX/CFQX Superfamily Signature.



ProDom Summary:  Protein Domain Search
Residues 312-432 are 74% similar to a defined domain of ATPA_MYCGA.
Residues 111-207 are 73% similar to a defined domain of ATPA_HELPY.


Paralogs:  Local Blast Search
UU132 is paralogously related to five proteins in U.urealyticum. For example: residues 34-417 are 38% similar to UU053, an ATP synthase alpha chain. Residues 624-799 are 43% similar to UU236, 50S ribosomal protein L22. Residues 86-367 are 26% similar to UU129, an ATP synthase beta chain. Residues 30-412 are 23% similar to UU054, an ATP synthase beta chain, and residues 512-676 are 20% similar to UU451, a hypothetical protein.


Pfam Summary:  Pfam Search
Residues 25 to 93 (E-value = 7e-14) place UU132 in the ATP-synt_ab_N family which is described as ATP synthase alpha/beta family, beta-barrel domain (PF02874)
Residues 191 to 371 (E-value = 7.8e-105) place UU132 in the ATP-synt_ab family which is described as ATP synthase alpha/beta family, nucleotide-binding domain (PF00006)
Residues 377 to 475 (E-value = 3.1e-12) place UU132 in the ATP-synt_ab_C family which is described as ATP synthase alpha/beta chain, C terminal domain (PF00306)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
1  
143
non-globular  
491  
743

PDB Hit:
gi|2981976|pdb|1SKY|B Chain B, Crystal Structure Of The Nucleotide Free Alpha3beta3 Sub-Complex Of F1-Atpase From The Thermophilic Bacillus Ps3

Gene Protein Sequence:
MTDNKNHSLISDIKSQIKKFSEKALTLEVGNVISLGDGIVLVDGLDNVML
NEIVRFENGVEGMALNLEEDAVGVVLLGDYSNIKEGDRVYRTKRIVEVPV
GDVMLGRVVDALGKAVDNKGNIVANKFSVIEKIAPGVMDRKSVHQPLETG
ILSIDAMFPIGKGQRELIIGDRQTGKTTIAIDAIINQKGRNVNCVYVAIG
QKNSTIANVVRELEAHGAMEYTTVVTANASELPALQYIAPFTGVTIAEEW
MHQGKDVLIVYDDLSKHAIAYRTLSLLLRRPPGREAYPGDVFYLHSRLLE
RACKLKDELGAGSITALPIIETQAGDISAYIPTNVISITDGQIFMMTSLF
NAGQRPAIDAGQSVSRVGSAAQIKSVKQTGASLKLELANYRELEAFSQFG
SDLDDETKRILKLGKAVMAVIKQAPNKPYNQTDEAIILFTVKEKLIPQVP
VERIQDFKEYLLNYFKGTKLRADLEDKKAFDKENTPAFRCAIQKAINSFL
NNSQDFKPCEEAEQTAFDKFFNENESIVVDGENDFNFINEEVSLKPTTET
SEAVQIEEKVQDFVEPQEILETNKMEENHIFEEVEPEKIICEHHEFEIAE
NQEKIEGQQVLEDTNHEYSIYETVEQSGEVDNDESKDDDLEVLVPVAEIE
HDEAILDERENRNWVFSDSAVSEVEKQTIMISISSNEAEQLFDNAKSVVF
FKVTPKYPVEKVLVYVTSPVQKVVGEFDLLKIDVNSVNTSWNKYRSSSVI
SSRKEYLEYFNSHKEAHALLASKVYKYRKPKDLASFNMNKGPSGFTYLK$


Gene Nucleotide Sequence:  Sequence Viewer
ATGACAGATAATAAAAATCATTCATTAATTAGTGATATAAAATCACAAAT
TAAGAAATTTTCTGAAAAAGCTTTAACCTTAGAGGTCGGCAATGTAATTT
CGTTAGGTGATGGAATTGTATTGGTTGATGGCCTTGATAATGTCATGTTA
AATGAAATTGTACGTTTTGAAAATGGTGTTGAAGGAATGGCTTTAAACCT
AGAAGAAGATGCTGTTGGTGTTGTTCTTTTAGGTGATTATTCAAATATTA
AAGAAGGCGATCGTGTTTATCGTACAAAAAGAATTGTTGAAGTTCCTGTT
GGGGATGTAATGTTAGGTCGTGTTGTTGACGCTTTAGGTAAGGCAGTTGA
TAATAAAGGTAATATTGTTGCAAATAAATTTAGTGTAATTGAAAAAATTG
CACCTGGTGTTATGGACCGTAAATCTGTTCATCAACCACTTGAAACCGGA
ATTTTATCAATTGATGCAATGTTCCCAATTGGTAAGGGCCAAAGAGAATT
AATTATTGGTGACCGACAGACTGGAAAAACAACAATTGCAATTGATGCTA
TTATTAATCAAAAAGGCCGTAATGTAAATTGTGTTTATGTAGCAATTGGT
CAAAAAAACTCAACAATCGCAAATGTTGTTCGTGAACTTGAAGCTCATGG
AGCAATGGAATATACAACTGTTGTTACAGCTAATGCTTCAGAATTACCTG
CTTTGCAATATATTGCTCCCTTTACAGGAGTAACAATTGCTGAAGAGTGA
ATGCATCAAGGAAAAGATGTTTTAATTGTTTATGATGATCTAAGCAAACA
TGCTATTGCTTATCGTACTTTATCCTTATTATTACGTCGTCCGCCTGGTC
GTGAAGCATATCCTGGAGATGTTTTTTACTTACACAGTCGTTTATTAGAA
CGTGCATGCAAACTAAAAGATGAATTAGGGGCAGGATCTATTACTGCTTT
ACCAATTATTGAAACACAAGCTGGTGATATTTCAGCTTATATTCCAACAA
ATGTAATTTCAATTACTGATGGGCAAATTTTTATGATGACATCATTATTT
AATGCTGGTCAACGTCCTGCAATTGATGCAGGGCAATCAGTTAGTCGGGT
AGGTTCTGCTGCACAAATTAAATCAGTTAAACAAACTGGAGCATCATTAA
AATTAGAATTAGCTAACTATCGCGAACTTGAAGCATTTAGTCAATTCGGT
AGTGATTTGGATGATGAAACTAAACGTATTCTAAAACTTGGTAAAGCAGT
TATGGCTGTTATTAAGCAAGCTCCTAATAAACCTTATAATCAAACTGATG
AAGCGATCATTTTGTTTACCGTTAAAGAAAAACTTATTCCTCAAGTTCCA
GTAGAACGTATTCAAGATTTTAAAGAGTACTTATTAAATTACTTTAAAGG
AACAAAACTACGTGCTGATCTTGAAGATAAGAAAGCTTTTGATAAAGAAA
ATACCCCAGCATTTAGATGTGCTATACAAAAAGCAATTAACAGTTTCTTA
AATAATTCACAAGATTTTAAACCTTGTGAAGAAGCTGAACAAACAGCCTT
TGATAAATTCTTTAATGAGAATGAATCAATTGTTGTTGATGGTGAAAATG
ATTTTAATTTTATTAATGAAGAAGTTAGTTTAAAACCTACAACAGAAACA
TCTGAAGCTGTTCAAATAGAAGAAAAAGTTCAAGATTTCGTTGAACCACA
AGAAATTCTTGAAACTAATAAAATGGAAGAAAATCATATTTTTGAAGAAG
TTGAGCCAGAAAAAATTATCTGTGAACATCATGAATTTGAAATAGCTGAA
AACCAAGAAAAAATCGAAGGTCAACAAGTTTTAGAAGATACAAACCATGA
ATATTCAATTTATGAAACCGTTGAACAAAGCGGTGAGGTAGATAATGATG
AATCTAAAGATGATGATTTAGAAGTCTTAGTACCAGTTGCTGAAATTGAG
CATGATGAAGCAATTCTAGATGAACGCGAGAATCGTAATTGAGTCTTCTC
AGATTCAGCTGTTTCTGAAGTTGAAAAACAAACAATTATGATTTCAATTT
CATCAAATGAAGCAGAACAATTGTTTGATAATGCTAAAAGTGTTGTTTTC
TTTAAAGTAACACCTAAATATCCAGTTGAAAAAGTATTAGTTTATGTCAC
AAGTCCAGTACAAAAAGTTGTTGGTGAATTTGATTTATTAAAGATTGATG
TTAATTCAGTAAACACTTCTTGAAATAAATATCGTTCAAGTTCAGTAATT
TCATCACGTAAAGAATATTTAGAATATTTTAACTCACACAAAGAAGCACA
TGCTTTATTAGCTTCTAAAGTTTATAAATATCGTAAGCCAAAAGATTTAG
CAAGTTTTAATATGAATAAAGGACCAAGTGGTTTCACTTATCTTAAATAA



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