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Ureaplasma urealyticum Search Results

Record: 1 of 1  
MiniMap tRNA-Gly-2 tRNA-Lys-1 tRNA-Gln-1 tRNA-Tyr-1 tRNA-Leu-1 rRNA_5S-2 rRNA_23S-2 IGR259 IGR257 IGR261 IGR258 IGR260 IGR262 IGR256 IGR255 rpS20, - UU310 ard1, - UU311 UU307 UU308 greA, - UU304 UU309 UU305 nfo, - UU306 rpS20, - UU310 ard1, - UU311 UU307 UU308 greA, - UU304 UU309 UU305 nfo, - UU306 Type: tandem, Name:  - 185 Type: tandem, Name:  - 190 Type: tandem, Name:  - 411 Type: tandem, Name:  - 184 Type: tandem, Name:  - 188 Type: tandem, Name:  - 182 Type: tandem, Name:  - 410 Type: tandem, Name:  - 189 Type: tandem, Name:  - 187 Type: tandem, Name:  - 183 Type: tandem, Name:  - 409 Type: tandem, Name:  - 186 rpS20, - UU310 ard1, - UU311 UU307 UU308 greA, - UU304 UU309 UU305 nfo, - UU306
* Calculated from Protein Sequence

Gene ID: UU306

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
nfo  

Definition:
endonuclease IV

Gene Start:
350885

Gene Stop:
351796

Gene Length:
912

Molecular Weight*:
34691

pI*:
8.20

Net Charge*:
5.37

EC:
3.1.21.2  

Functional Class:
replication; DNA replication, restriction, modification, recombination, and repair  

Pathway: pathway table

Comment:
DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3'terminus of DNA strand breaks.

See Prosite PDOC00599.

From Prosite:

DNA damaging agents such as the antitumor drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3'termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3'terminus of DNA strand breaks.


Blast Summary:  PSI-Blast Search
Several hits in gapped BLAST to END4 proteins, e.g. residues 6-294 are 45% similar to END4_BACSU. Some similarities to eukaryotic APN1s. UU306 is similar to MG235 and CT625, both predicted endonuclease IV sequences. No similarity to T.pallidum.

COGS Summary:  COGS Search
The phylogenetic pattern of COG0648 is EHgpcMy-.
Cog name: Endonuclease IV and related predicted endonucleases.
Functional class: L.
BeTs to e--p-my-.
Number of proteins in this genome belonging to this COG is 1



Blocks Summary:  Blocks Search
Residues 71-268 span five regions of similarity to blocks BL00729A-E, encompassing AP endonuclease family sequences, e.g. END4_MYCGE, END4_BACSU.


ProDom Summary:  Protein Domain Search
Residues 59-267 are 46% similar to an endonuclease domain of END4_MYCGE.
Residues 6-68 are 47% similar to an endonuclease domain of END4_BACSU.

Paralogs:  Local Blast Search
No paralogs in U.u.

Pfam Summary:  Pfam Search
Residues 8 to 244 (E-value = 8e-90) place UU306 in the AP_endonuc_2 family which is described as AP endonuclease family 2 (PF01261)

PDB Hit:
gi|6137712|pdb|1QUM|A Chain A, Crystal Structure Of Escherichia Coli Endonuclease Iv In Complex With Damaged Dna

Gene Protein Sequence:
MDKYNLIIGSHVSLKAKDFFYGSVKEALSYGSNTFMVYTGAPQNTKRQPI
KSFKIEEAHNLLKKHNINLDDLIVHAPYIINPCSSKKNVRELAKEFLIQE
IQRTESMGITKLVLHPGSRLEQNEDIALEQVYTMLNDIFSTINTNVIVCL
ETMAGKGSEIGVNIKQLKTIIDNVHSKKNIGVCLDTCHMNDSGLILDYYN
FNQYLKEFDAQIGINYIKVLHINDSKNPCGANKDRHENLGYGTIGFANLI
NIIYHPLLNNIPKILETPWFNVNDELIPLYKHEIKMIRDCKWYDIKNKLL
SKK$

Gene Nucleotide Sequence:  Sequence Viewer
ATGGATAAATATAATTTAATTATAGGTAGTCATGTAAGTTTAAAAGCTAA
AGATTTCTTTTATGGTAGTGTAAAAGAAGCATTATCTTATGGTTCTAACA
CGTTTATGGTTTATACTGGAGCTCCACAAAATACAAAACGTCAACCGATT
AAATCATTTAAAATTGAAGAAGCACATAATTTGTTAAAAAAACATAATAT
TAATTTGGATGATTTAATTGTTCACGCTCCATATATTATCAACCCTTGTT
CTTCTAAAAAGAATGTTCGTGAACTTGCTAAAGAATTTTTAATTCAGGAA
ATCCAACGAACAGAATCTATGGGGATCACTAAACTTGTTTTACATCCAGG
ATCACGTTTAGAACAAAATGAAGATATAGCTTTAGAACAAGTTTATACAA
TGTTAAATGATATTTTTTCAACTATTAATACTAATGTAATTGTTTGCTTA
GAGACCATGGCTGGTAAAGGTTCTGAAATTGGGGTAAATATAAAACAATT
AAAAACCATTATAGACAATGTTCATTCTAAAAAAAATATTGGCGTTTGTT
TAGATACTTGCCATATGAATGATAGCGGTTTGATTTTAGATTATTATAAT
TTTAATCAATATTTAAAAGAATTTGATGCACAAATTGGTATTAATTATAT
TAAAGTATTACATATTAACGATTCTAAAAACCCTTGTGGTGCAAACAAAG
ACCGCCACGAAAATTTAGGATATGGAACGATAGGTTTTGCAAATTTAATT
AATATTATTTACCATCCCTTATTAAATAACATCCCTAAAATTTTAGAAAC
GCCTTGGTTTAATGTTAATGATGAATTAATTCCTTTATATAAGCATGAAA
TAAAAATGATTCGCGACTGCAAGTGGTATGACATTAAAAACAAATTATTA
TCGAAGAAATAA


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