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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0292 IGR0288 IGR0289 IGR0293 IGR0295 IGR0290 IGR0287 IGR0291 IGR0285 IGR0284 IGR0286 IGR0294 pfs, - NG0345 lepB, - NG0343 lepA, - NG0344 NG0350 NG0351 NG0354 pilZ, - NG0348 tpn, - NG0355 upp, - NG0353 NG0349 NG0356 holB, - NG0347 pilT, - NG0346 pfs, - NG0345 lepB, - NG0343 lepA, - NG0344 NG0350 NG0351 NG0354 pilZ, - NG0348 tpn, - NG0355 upp, - NG0353 NG0349 NG0356 holB, - NG0347 pilT, - NG0346 pfs, - NG0345 lepB, - NG0343 lepA, - NG0344 NG0354 pilZ, - NG0348 tpn, - NG0355 upp, - NG0353 NG0349 NG0356 holB, - NG0347 pilT, - NG0346 NG0352 NG0351 NG0350 NG0352
* Calculated from Protein Sequence

Gene ID: NG0347

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
holB  

Definition:
DNA polymerase III, delta prime subunit

Gene Start:
342669

Gene Stop:
343643

Gene Length:
975

Molecular Weight*:
36999

pI*:
8.30

Net Charge*:
6.33

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:
Dong,Z., Onrust,R., Skangalis,M. and O'Donnell,M. DNA polymerase III accessory proteins. I. holA and holB encoding delta and delta'. J. Biol. Chem. 268 (16): 11758-11765 (1993) [Medline: 93280136].

Carter,J.R., Franden,M.A., Aebersold,R. and McHenry,C.S. Identification, isolation, and characterization of the structural gene encoding the delta' subunit of Escherichia coli DNA polymeraseIII holoenzyme. J. Bacteriol. 175 (12): 3812-3822 (1993) [Medline: 93285995].

Onrust,R. and O'Donnell,M. DNA polymerase III accessory proteins. II. Characterization of delta and delta'. J. Biol. Chem. 268 (16): 11766-11772 (1993) [Medline: 9328013].

Guenther,B., Onrust,R., Sali,A., O'Donnell,M. and Kuriyan,J. Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III. Cell 91 (3): 335-345 (1997) [Medline: 98028572].

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

Comment:
Oklahoma ID: NGO.347

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), NG0002 (beta), NG0283 (delta), NG0743 (gamma-tau), NG0973 (epsilon), NG1226 (chi).

Blast Summary:  PSI-Blast Search
NG0347 is orthologously related to AE002431, Neisseria meningitidis, strain MC58, a putative DNA polymerase III, delta prime subunit protein: residues 1-324 are 93% similar to residues 1-324 of NG0347.

Numerous significant hits to DNA polymerase proteins in gapped BLAST; e.g. residues 2-251 are 37% similar to gb|AAG06349.1|AE004722_5 DNA polymerase III, delta prime subunit of Pseudomonas aeruginosa, residues 2-220 are 33% similar to gb|AAF95163.1| DNA polymerase III, delta prime subunit of Vibrio cholerae, residues 2-261 are 33% similar to 1074027 DNA-directed DNA polymerase III delta' chain homolog of Haemophilus influenzae.

COGS Summary:  COGS Search
BeTs to 15 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 3-122 are 36% similar to a (PROTEIN DNA POLYMERASE III DELTA' SUBUNIT TRANSFERASE) protein domain (PD022233) which is seen in HOLB_PSEAE.

Residues 66-254 are 31% similar to a (DNA III PROTEIN POLYMERASE) protein domain (PD035127) which is seen in P74389_SYNY3.

Residues 123-164 are 64% similar to a (DNA POLYMERASE III DELTA') protein domain (PD190814) which is seen in HOLB_PSEAE.

Residues 22-148 are 40% similar to a (PROTEIN ATP-BINDING PROTEASE SUBUNIT REGULATORY HOMOLOG) protein domain (PD000092) which is seen in O67707_AQUAE.



Paralogs:  Local Blast Search


NG0347 is paralogously related to NG0743 (DNA polymerase III tau and gamma chains) (2e-20).


Pfam Summary:  Pfam Search
No significant hits to the Pfam 11.0 database

Structural Feature(s):
Feature Type  Start  Stop
non-globular  
166  
257

PDB Hit:
pdb|1A5T|1A5T CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF 105.0 1e-23
pdb|1JR3|1JR3-A CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP 94.8 2e-20
pdb|1IQP|1IQP-A CRYSTAL STRUCTURE OF THE CLAMP LOADER SMALL 42.2 1e-04
pdb|1A5T|1A5T CRYST

Gene Protein Sequence:
MIYPWHQEQWRQIAEHWTSRPNAWLFVGKKGTGKTAFARFAAKALLCETP
APGCKPCGECMSCHLFGRGSHPDFYEITPLADEPENGRKLLRIKIDAVRE
IIDNVYLTSVRGGLRVILIHPAESMNVQAANSLLKVLEEPPPQVVFLLVS
HAADKVLPTIKSRCRKMVLPAPSHGEALAYLRDRGVAEPEERLAFHSGAP
LFQEEGELRELRAKLLEILAEPRLLKILDYAALFDKEKLPLAVFVGWMQK
WLVDLGLCLQHMKPVYYPAYEDRLLQTASGFRPRNVFAAEDMLKQLAPYG
FHTLNVKMQIEHLLINYLELKKENR

Gene Nucleotide Sequence:  Sequence Viewer
ATGATTTATCCGTGGCATCAGGAACAATGGCGGCAGATTGCCGAGCATTG
GACGAGCCGTCCTAATGCGTGGCTGTTTGTTGGCAAAAAGGGGACGGGGA
AGACTGCGTTTGCCCGCTTTGCGGCGAAGGCGCTGTTGTGCGAAACCCCT
GCACCGGGCTGCAAACCCTGTGGCGAATGTATGTCCTGCCATCTGTTTGG
ACGGGGAAGCCATCCCGATTTTTACGAAATCACGCCTCTGGCGGACGAAC
CCGAAAACGGACGCAAACTGTTGCGGATCAAAATCGATGCCGTCAGGGAA
ATCATCGATAATGTGTACCTGACTTCGGTACGGGGCGGTTTGCGCGTGAT
CCTGATTCATCCTGCGGAAAGTATGAATGTCCAAGCCGCCAACAGTTTGT
TGAAAGTGTTGGAAGAGCCGCCGCCACAAGTGGTCTTTTTGCTGGTAAGC
CACGCGGCGGACAAGGTTTTACCGACCATTAAAAGCCGCTGCCGGAAGAT
GGTTTTGCCCGCTCCTTCGCATGGGGAAGCATTGGCGTATCTGCGCGACA
GGGGTGTGGCGGAGCCTGAGGAACGTCTGGCTTTCCATTCGGGTGCGCCG
CTGTTTCAGGAGGAAGGCGAGCTTCGGGAATTGAGGGCAAAGCTGCTGGA
GATATTGGCAGAGCCGAGATTGTTGAAGATTTTGGATTACGCCGCGCTTT
TCGATAAGGAAAAACTTCCGCTCGCCGTATTTGTCGGGTGGATGCAGAAA
TGGCTGGTCGATTTAGGCTTGTGCCTGCAACACATGAAACCCGTCTATTA
TCCCGCTTATGAAGACAGGCTGCTTCAGACGGCATCGGGTTTCCGTCCGC
GCAATGTATTTGCGGCGGAGGATATGCTCAAACAGCTTGCCCCTTACGGG
TTTCATACTTTAAATGTCAAAATGCAGATCGAGCATCTGCTCATCAACTA
TTTGGAATTGAAGAAAGAGAACAGG


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