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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0623 IGR0622 IGR0616 IGR0624 IGR0619 IGR0620 IGR0621 IGR0617 IGR0618 NG0742 aroD, - NG0740 mutL,hexB, - NG0744 rep, - NG0739 dp3x, - NG0743 NG0745 purE,pur6, - NG0748 camT, - NG0746 NG0747 recA, - NG0741 NG0742 aroD, - NG0740 mutL,hexB, - NG0744 rep, - NG0739 dp3x, - NG0743 NG0745 purE,pur6, - NG0748 camT, - NG0746 NG0747 recA, - NG0741 NG0742 aroD, - NG0740 mutL,hexB, - NG0744 rep, - NG0739 dp3x, - NG0743 camT, - NG0746 NG0747 recA, - NG0741 NG0745 purE,pur6, - NG0748
* Calculated from Protein Sequence

Gene ID: NG0743

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
dp3x  

Definition:
DNA polymerase III tau and gamma chains

Gene Start:
741419

Gene Stop:
739299

Gene Length:
2121

Molecular Weight*:
76076

pI*:
4.60

Net Charge*:
-38.44

EC:
2.7.7.7  

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

Pathway: pathway table
DNA polymerase
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Blinkowa,A.L. and Walker,J.R. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res. 18 (7): 1725-1729 (1990) [Medline: 90245560].

Tsuchihashi,Z. and Kornberg,A. Translational frameshifting generates the gamma subunit of DNA polymerase III holoenzyme. Proc. Natl. Acad. Sci. U.S.A. 87 (7): 2516-2520 (1990) [Medline: 90207226].

Comment:
The Neisseria sp. have very long (>700 amino acids) DNA polymerase III tau and gamma chain proteins in comparison to other organisms. The last 200 amino acids of this protein only hit to a protein from N.meningitidis. Subthreshold hits to this C-terminal region match to proteinases (ie: Streptococcus pneumoniae immunoglobulin protease, e-03; Haemophilus influenzae IgA protease, 2e-03).

From GenBANK (gi:118808): DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The tau chain serves as a scaffold to help in the dimerizaton of the core complex. The gamma chain seems to interact with the delta subunit to transfer the beta subunit on the DNA. The reaction: N deoxynucleoside triphosphate = N pyrophosphate + DNA(N). The enzyme contains a core (composed of alpha, epsilon, and theta chains) that associates with a tau subunit which allow the core dimerization to form the PolIII' complex. PolIII' associates with the gamma complex (composed of chains gamma, delta, delta', psi, and chi) and with the beta chain. The final composition of the complex is: (alpha,epsilon,theta)[2]-tau[2]-(gamma,delta,delta', psi,chi)[2]-beta[4]. The production of the two protein products from this region is due to programmed ribosomal frameshifting. Partial similarity to phage T4 DNA polymerase accessory protein 44 and to human activator 1, 37 and 40 kda subunits.

For a review of DNA Pol III, see O'Donnell,M. Accessory protein function in the DNA polymerase III holoenzyme from E. coli. Bioessays 14 (2), 105-111 (1992) Medline: 92246902.

For other pol III subunits, see NG0078 (alpha), NG0283 (delta), NG0347 (delta prime), NG0002 (beta), NG0973 (epsilon), NG1226 (chi).

Oklahoma ID: NGO.743c

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to DNA polymerase III tau and gamma chains; e.g. residues 1-363 are 57% similar to 11348451 of Pseudomonas aeruginosa.

NG0743 is orthologous to AL162756, N. meningitidis Z2491 DNA polymerase III tau and gamma chains: residues 1-709 have 88% similarity to residues 1-707 in NG0743.

COGS Summary:  COGS Search
BeTs to 17 clades of COG0470
COG name: ATPase involved in DNA replication
Functional Class:  L
The phylogenetic pattern of COG0470 is AMTKYQVCEBRHUJGPOLINX
Number of proteins in this genome belonging to this COG is 2

Blocks Summary:  Blocks Search
No significant hits to the Blocks database.

ProDom Summary:  Protein Domain Search
Residues 63-158 are 36% similar to a (PUTATIVE DNA POLYMERASE III) protein domain (PD098254) which is seen in O64728_ARATH.

Residues 39-127 are 35% similar to a (PROTEIN DNA POLYMERASE III DELTA' SUBUNIT TRANSFERASE) protein domain (PD022233) which is seen in O06363_MYCTU.

Residues 21-90 are 42% similar to a (DNA POLYMERASE III, DELTA') protein domain (PD022234) which is seen in HOLB_BACSU.

Residues 161-270 are 49% similar to a (PROTEIN SUBUNIT REPLICATION DNA ATP-BINDING FACTOR C) protein domain (PD001148) which is seen in DP3X_ECOLI.

Residues 101-185 are 38% similar to a (DNA III PROTEIN POLYMERASE) protein domain (PD035127) which is seen in O67486_AQUAE.

Residues 6-62 are 71% similar to a (PROTEIN DNA ATP-BINDING SUBUNIT) protein domain (PD000893) which is seen in DP3X_HAEIN.

Residues 72-127 are 58% similar to a (DNA III POLYMERASE TAU) protein domain (PD004595) which is seen in DP3X_ECOLI.

Residues 129-159 are 83% similar to a (DNA III POLYMERASE SUBUNIT) protein domain (PD186244) which is seen in DP3X_ECOLI.

Residues 15-157 are 60% similar to a (PROTEIN ATP-BINDING PROTEASE SUBUNIT REGULATORY HOMOLOG) protein domain (PD000092) which is seen in O67707_AQUAE.



Paralogs:  Local Blast Search


NG0743 is paralogously related to NG0347 (DNA polymerase III, delta prime subunit) (4e-20), NG0696 (conserved hypothetical protein) (2e-18) and NG0760 (Holliday junction DNA helicase RuvB) (1e-05).


Pfam Summary:  Pfam Search
Residues 40 to 230 (E-value = 3.6e-09) place NG0743 in the AAA family which is described as ATPase family associated with various cellular activities (AAA) (PF00004)

Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
258  
291
transmembrane  
282  
298
transmembrane  
348  
364
non-globular  
356  
576
non-globular  
613  
707

PDB Hit:
pdb|1JR3|1JR3-A CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP 392.0 0e+00
pdb|1IQP|1IQP-A CRYSTAL STRUCTURE OF THE CLAMP LOADER SMALL 111.0 3e-25
pdb|1A5T|1A5T CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF 97.1 9e-21
pdb|1IN7|1IN7-A THER

Gene Protein Sequence:
MAYQVLARKWRPKTFSDLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVG
KTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTG
IDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKSAFNAMLKTLEEPPEHV
KFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYDP
PALQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDVRQMIGAVDKQYLY
ELLTGIVNQDGEALLAKAQEMAACAVGFDNALGELAILLQQLALIQAVPS
ALAHDDPDSDILHRLAQTISGEQIQLYYQIAVHGKRDLGLAPDEYAGFMM
TLLRMLAFAPLAAASCDANAVIENTELQSPSAQTAEKETAAKKPQPRPEA
DAAQTPVQTASAAAMPSEGKTAGPVSHQENNDVPPWEDAPDKTETAAGTA
RTSAKSIQTASEAETPPENQVSKNKAADNETEASLSEVPSENPIQATPND
EAVETETFAHEAPAEPFYGFPDNDCPPEDGVEIPPPDWANVLPADTAGGG
TDEEAEAGGIGGNNTPSAPPPEFSTENWAAIVRHFARKLGAAQMPAQHSA
WTEYRSDTGLMVLAMTAEARATADKKRLDKIRDTLAQAYGLQLTLQTEDW
RDEAGRETPAMQDKRVQAEDRQKAQALLEADPAAQKILQAFGAQWQPESL
ELAANRP

Gene Nucleotide Sequence:  Sequence Viewer
ATGGCCTATCAAGTTCTCGCCCGAAAATGGCGGCCCAAAACCTTTTCCGA
CTTAGTCGGTCAGGAACACGTCGTCAAAGCCCTGCAAAATGCCTTGGACG
AAGGCAGGCTGCACCACGCCTACCTGCTGACCGGGACGCGCGGCGTGGGC
AAAACCACCATCGCCCGCATCCTTGCCAAAAGCCTCAACTGCGAAAATGC
GCAACACGGCGAACCTTGCGGCGTGTGCCAAAGCTGCACCCAAATCGATG
CCGGACGCTATGTCGACCTGCTCGAAATCGACGCCGCCTCCAACACAGGC
ATCGACAACATCCGCGAAGTCTTGGAAAACGCCCAATACGCGCCGACCGC
CGGCAAATACAAAGTCTATATCATCGACGAAGTGCATATGCTTTCCAAAA
GCGCGTTCAACGCCATGCTCAAAACGCTGGAAGAGCCGCCCGAACACGTC
AAATTCATCCTCGCCACCACCGATCCGCACAAAGTCCCCGTTACCGTATT
AAGCCGCTGCCTACAATTCGTCTTACGCAATATGACCGCGCAACAGGTTG
CCGACCACCTTGCCCACGTCCTCGACAGCGAAAAAATCGCCTACGACCCC
CCCGCCCTGCAACTTTTGGGACGTGCCGCCGCCGGATCGATGCGCGATGC
CTTAAGCCTGCTCGACCAAGCCATCGCCCTAGGTTCGGGCAAAGTTGCCG
AAAACGATGTCCGCCAAATGATCGGCGCGGTTGACAAACAATACCTGTAC
GAACTGCTGACAGGCATCGTCAACCAAGACGGCGAAGCCCTGCTGGCAAA
AGCGCAGGAAATGGCGGCGTGTGCCGTCGGCTTTGACAACGCCTTGGGCG
AACTGGCCATACTGCTGCAACAACTCGCCCTGATACAGGCAGTCCCCTCC
GCCTTGGCGCACGACGACCCCGATTCCGATATTTTGCACCGCCTCGCCCA
AACCATAAGCGGCGAACAAATCCAGCTTTACTACCAAATCGCCGTCCACG
GCAAACGCGACCTGGGCCTCGCCCCCGACGAATACGCCGGCTTTATGATG
ACCCTGCTGCGTATGCTGGCGTTCGCCCCCTTGGCGGCGGCTTCGTGTGA
TGCAAACGCCGTGATTGAAAATACCGAACTTCAATCCCCGTCGGCACAAA
CCGCCGAAAAGGAAACCGCCGCAAAAAAGCCACAACCGCGCCCTGAAGCG
GATGCCGCCCAAACGCCCGTTCAGACGGCATCCGCAGCAGCAATGCCGTC
TGAAGGCAAAACTGCCGGCCCCGTTTCCCATCAAGAAAACAACGATGTTC
CGCCTTGGGAAGACGCGCCGGACAAAACCGAAACCGCAGCCGGCACGGCG
CGAACGTCGGCAAAAAGCATTCAGACGGCATCCGAAGCCGAAACGCCGCC
CGAAAATCAAGTTTCCAAGAACAAGGCAGCCGACAACGAAACCGAGGCTT
CCTTGTCCGAAGTGCCGTCTGAAAACCCCATTCAGGCAACACCGAATGAT
GAAGCCGTTGAAACGGAAACATTTGCACACGAAGCCCCTGCAGAACCTTT
CTACGGTTTTCCGGATAATGACTGCCCCCCGGAAGACGGCGTGGAAATCC
CGCCGCCCGATTGGGCAAATGTCCTCCCTGCCGATACCGCAGGCGGAGGG
ACGGACGAAGAAGCAGAAGCGGGCGGCATCGGCGGAAACAACACGCCGTC
CGCCCCGCCGCCCGAATTTTCCACCGAAAACTGGGCAGCCATCGTCCGGC
ACTTCGCCCGCAAACTCGGCGCGGCGCAAATGCCGGCGCAACACTCCGCG
TGGACGGAATACCGTTCCGACACCGGACTGATGGTTTTGGCAATGACCGC
CGAAGCCCGCGCCACCGCCGACAAAAAGCGGCTCGACAAAATCCGCGACA
CCCTCGCCCAAGCCTACGGGCTGCAACTCACCCTGCAAACCGAAGACTGG
CGCGACGAAGCCGGCCGGGAAACCCCCGCGATGCAGGACAAGCGTGTCCA
AGCCGAAGACAGGCAAAAAGCACAAGCATTGCTCGAAGCCGACCCCGCCG
CACAAAAAATCCTCCAAGCATTCGGCGCGCAATGGCAGCCCGAATCACTG
GAATTGGCGGCAAACCGGCCA


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