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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0236 IGR0238 IGR0235 IGR0234 IGR0239 IGR0240 IGR0237 IGR0233 IGR0240.1 IGR0233.1 IGR0241 NG0280 comL, - NG0277 NG0279 rpoH, - NG0288 NG0286 lnt, - NG0289 NG0284 NG0287 NG0282 NG0285 NG0281 holA, - NG0283 rluD, - NG0278 NG0280 comL, - NG0277 NG0279 rpoH, - NG0288 NG0286 lnt, - NG0289 NG0284 NG0287 NG0282 NG0285 NG0281 holA, - NG0283 rluD, - NG0278 NG0280 comL, - NG0277 NG0279 rpoH, - NG0288 NG0286 lnt, - NG0289 NG0287 NG0282 NG0285 NG0281 holA, - NG0283 rluD, - NG0278 NG0284
* Calculated from Protein Sequence

Gene ID: NG0283

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
holA  

Definition:
DNA polymerase III, delta subunit

Gene Start:
284543

Gene Stop:
285538

Gene Length:
996

Molecular Weight*:
36192

pI*:
5.60

Net Charge*:
-4.10

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:
Carter,J.R., Franden,M.A., Aebersold,R. and McHenry,C.S. 1992. Molecular cloning, sequencing, and overexpression of the structural gene encoding the delta subunit of Escherichia coli DNA polymerase III holoenzyme. J. Bacteriol. 174 (21): 7013-7025. Medline: 93015766.
Dong,Z., Onrust,R., Skangalis,M. and O'Donnell,M. 1993. DNA polymerase III accessory proteins. I. holA and holB encoding
delta and delta'. J. Biol. Chem. 268 (16): 11758-11765. Medline: 93280136.


Comment:
Oklahoma ID: NGO.283

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), NG0347 (delta prime), NG0743 (gamma-tau), NG0973 (epsilon), NG1226 (chi).

Blast Summary:  PSI-Blast Search
NG0283 is orthologously related to AE002425, Neisseria
meningitidis, strain MC58, a DNA polymerase III, delta subunit protein: residues 1-332 are 96% similar to residues 1-332 of NG0283.

Several significant hits to DNA polymerase III, delta subunit proteins in gapped BLAST; e.g. residues 13-320 are 41% similar to gb|AAG07376.1|AE004816_12 DNA polymerase III, delta subunit of Pseudomonas aeruginosa, residues 5-332 are 32% similar to gb|AAF84977.1|AE004031_9 DNA polymerase III, delta subunit of Xylella fastidiosa, residues 14-326 are 28% similar to gb|AAF94115.1| DNA polymerase III, delta subunit of Vibrio cholerae.

COGS Summary:  COGS Search
No hits to the COGs database.

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

ProDom Summary:  Protein Domain Search
Residues 7-330 are 23% similar to a (DNA POLYMERASE III DELTA) protein domain (PD041218) which is seen in HOLA_ECOLI.



Paralogs:  Local Blast Search


NG0283 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 7 to 332 (E-value = 6.8e-27) place NG0283 in the DNA_pol3_delta family which is described as DNA polymerase III, delta subunit (PF06144)

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
82  
219

PDB Hit:
pdb|1JQJ|1JQJ-C MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE 108.0 2e-24
pdb|1JQL|1JQL-B MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE 63.2 6e-11
pdb|1JQJ|1JQJ-C MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE 471.0 0e+00
pdb|1JQL|1JQL-B MECH

Gene Protein Sequence:
VAAHIGRIDTDAPLKPLYVIHGEEELLRIEAVDALRAAAKKQGYLNREAY
TADASFDWNELLQTAGNAGLFADLKLLELHIPNGKPGKNGGEALQDFAAR
LPEDTVTLVLLPKLEKTRLQSKWFAALAAKGEVWEAKPVGAAALPQWIRG
RLDKIGLGIEADALALFAERVEGNLLAARQEIDKLALLYPKGHAVNIDEA
QTAVANVARFDAFQLAGAWMKGDVPRVCRLLDGLEEEGEEPVLLLWAVAE
DVRTLIRLAAALKQGQSIQSVRNSLRLWGDKQTLAPLAVKRISVVRLLDA
LKTCAQIDRIIKGAEDGDAWTVFKQLVVSLAE

Gene Nucleotide Sequence:  Sequence Viewer
GTGGCGGCACATATCGGACGCATCGATACGGACGCGCCTTTGAAACCTCT
GTACGTCATCCACGGCGAGGAAGAACTGCTGCGTATCGAGGCAGTGGACG
CATTGAGGGCGGCGGCGAAGAAGCAGGGTTATCTCAACCGCGAAGCCTAT
ACCGCCGACGCGTCTTTCGATTGGAACGAACTGCTGCAAACCGCAGGCAA
TGCGGGTCTGTTTGCCGATTTGAAACTGTTGGAACTGCATATCCCCAACG
GAAAACCCGGCAAAAACGGCGGCGAGGCATTGCAGGATTTTGCCGCCCGA
CTGCCGGAAGATACGGTAACGCTGGTTTTGCTGCCCAAACTGGAGAAAAC
CCGGCTCCAGTCCAAATGGTTTGCCGCATTGGCGGCAAAGGGGGAAGTAT
GGGAAGCCAAACCGGTCGGTGCGGCGGCTTTGCCCCAATGGATACGCGGA
CGGCTGGACAAAATCGGTTTGGGTATCGAGGCAGACGCATTGGCACTGTT
TGCCGAGCGCGTGGAAGGCAATCTGTTGGCGGCACGTCAGGAAATCGACA
AGCTCGCGCTGCTGTATCCGAAAGGGCATGCCGTCAATATCGATGAGGCG
CAAACCGCCGTTGCCAATGTTGCCCGCTTCGACGCGTTCCAACTGGCAGG
CGCGTGGATGAAGGGCGATGTCCCGCGCGTATGCAGGCTGTTGGACGGGT
TGGAGGAAGAAGGCGAAGAACCGGTGCTGCTTCTGTGGGCGGTTGCCGAA
GACGTGCGGACGCTGATTCGGCTTGCCGCTGCCCTGAAACAGGGGCAGAG
CATCCAATCCGTCCGCAACAGCCTCAGGCTTTGGGGCGACAAACAGACGC
TCGCACCGCTTGCGGTCAAGCGGATTTCCGTCGTCCGCCTGCTTGACGCG
CTCAAAACCTGCGCCCAAATCGACCGAATCATCAAAGGCGCGGAAGACGG
CGACGCATGGACGGTATTCAAACAGCTTGTCGTGTCGCTGGCGGAA


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