Basic Search | Intermediate Search | Advanced SQL Search | Gene Image Map |  Home

Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR1797 IGR0005 IGR1795 IGR1794 IGR1796 IGR0002 IGR0003 IGR0004 IGR0005.1 IGR0001 rl34, - NG2182 NG2180 NG0005 rnpA, - NG2181 NG0004 NG2178 ppk, - NG0003 NG2179 dnaN, - NG0002 dnaA, - NG0001 leuS, - NG0006 rl34, - NG2182 NG2180 NG0005 rnpA, - NG2181 NG0004 NG2178 ppk, - NG0003 NG2179 dnaN, - NG0002 dnaA, - NG0001 leuS, - NG0006 rnpA, - NG2181 NG0004 NG2178 ppk, - NG0003 rl34, - NG2182 NG2180 NG0005 NG2179 dnaN, - NG0002 dnaA, - NG0001 leuS, - NG0006
* Calculated from Protein Sequence

Gene ID: NG0002

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
dnaN  

Definition:
DNA polymerase III beta subunit

Gene Start:
1795

Gene Stop:
2895

Gene Length:
1101

Molecular Weight*:
40857

pI*:
4.90

Net Charge*:
-8.39

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:
Fujita,M.Q., Yoshikawa,H. and Ogasawara,N.
Structure of the dnaA region of Pseudomonas putida: conservation
among three bacteria, Bacillus subtilis, Escherichia coli and P.
putida.
Mol. Gen. Genet. 215 (3), 381-387 (1989).
Medline: 89218947.

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.02

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 'dna' genes, see NG0001 (dnaA), NG0078 (dnaE), NG0235 (dnaJ), NG0451 (dnaB), NG0485 (dnaB), NG0551 (dnaJ), NG0973 (dnaQ), NG0998 (dnaG), NG1110 (dnaC), NG1429 (dnaK), NG1636 (dnaC) and NG1901 (dnaJ). For other pol III subunits, see NG0078 (alpha), NG0283 (delta), NG0347 (delta prime), NG0743 (gamma-tau), NG0973 (epsilon), NG1226 (chi).

Blast Summary:  PSI-Blast Search
Numerous hits in gapped BLAST to DNA polymerase III beta chain sequences, e.g. residues 7-367 are 42% similar to the enzyme from P.putida (X14791). Residues 1-367 are 94% similar to the predicted dnaN protein in N.meningitidis (AL162753).

COGS Summary:  COGS Search
BeTs to 12 clades of COG0592
COG name: DNA polymerase III beta subunit
Functional Class:  L
The phylogenetic pattern of COG0592 is amtKyqvcebrhujgpolinx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB001001 (DNA polymerase III, beta chain) with a combined E-value of 1.1e-75.
    IPB001001A    6-54
    IPB001001B    66-80
    IPB001001C    99-117
    IPB001001D    136-159
    IPB001001E    170-180
    IPB001001F    194-204
    IPB001001G    235-250
    IPB001001H    313-332
    IPB001001A    131-179
    IPB001001H    63-82


ProDom Summary:  Protein Domain Search
Residues 7-168 are 44% similar to a (DNA III BETA CHAIN) protein domain (PD003730) which is seen in DP3B_PSEPU.

Residues 171-366 are 40% similar to a (DNA III BETA CHAIN POLYMERASE TRANSFERASE DNA-DIRECTED) protein domain (PD003062) which is seen in DP3B_PSEPU.



Paralogs:  Local Blast Search


NG0002 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 2 to 120 (E-value = 5.2e-28) place NG0002 in the DNA_pol3_beta family which is described as DNA polymerase III beta subunit, N-terminal domain (PF00712)
Residues 130 to 244 (E-value = 1.4e-39) place NG0002 in the DNA_pol3_beta_2 family which is described as DNA polymerase III beta subunit, central domain (PF02767)
Residues 246 to 366 (E-value = 1.7e-38) place NG0002 in the DNA_pol3_beta_3 family which is described as DNA polymerase III beta subunit, C-terminal domain (PF02768)

Structural Feature(s):
Feature Type  Start  Stop
No predicted structural features.  
  

PDB Hit:
pdb|2POL|2POL-A POL III (BETA SUBUNIT) (E.C.2.7.7.7) 261.0 1e-70
pdb|1JQJ|1JQJ-A MECHANISM OF PROCESSIVITY CLAMP OPENING BY THE 257.0 2e-69
pdb|2POL|2POL-A POL III (BETA SUBUNIT) (E.C.2.7.7.7) 262.0 9e-71
pdb|1JQJ|1JQJ-A MECH

Gene Protein Sequence:
MLILQAERDSLLKPLQAFTGIVERLHTLPILSNVLIEGRGGQTKLLATDL
EIQIDTAGPEGGAGDFRITTNAKKFQDILRALPAGALVSLDWDDNRLTLK
AGKSRFALQTLPAADFPMMNVGEDISATFSLGQERFKTMLSQVQYSMAVQ
DIRYYLNGLLMQVEGSQLRLVATDGHRLAYAACAIDADLPRAEVILPRKT
VLELFKLLNNPDDPIQIELLDKQVRFQCNGTTIVSKVIDGKFPDFNRVIP
LDNDKIFVLSRAELLGALERVSILANEKFRGARLFLQPGLLSVVCSNNEQ
EEAREEIEIAYQGGELEVGFNIGYLMDVLRNIHSDDMQLAFGDANRSTLF
TVPNNPNFKYIVMPMRI

Gene Nucleotide Sequence:  Sequence Viewer
ATGTTGATTTTACAAGCCGAGCGCGACAGCCTGCTCAAGCCGCTGCAAGC
CTTTACCGGCATCGTCGAACGCCTACACACCCTGCCCATCCTGTCCAATG
TGCTGATTGAGGGCAGGGGCGGTCAGACCAAACTCTTGGCAACCGATTTG
GAAATCCAAATCGACACCGCGGGTCCCGAGGGAGGTGCGGGCGACTTCCG
CATCACTACCAATGCCAAGAAATTTCAGGACATTTTGCGCGCGCTGCCTG
CCGGTGCGCTGGTGTCGCTGGATTGGGACGACAACCGTCTGACGCTGAAG
GCGGGCAAATCGCGTTTTGCCCTGCAAACCCTGCCTGCCGCCGATTTTCC
GATGATGAATGTCGGCGAGGACATCAGCGCGACTTTCTCGCTGGGGCAGG
AGCGTTTCAAAACCATGCTGTCGCAAGTGCAGTACAGCATGGCGGTGCAG
GACATCCGCTATTATCTCAACGGTCTGCTGATGCAGGTTGAGGGCAGCCA
GTTGCGCCTTGTGGCGACCGACGGACACCGCCTTGCCTATGCAGCCTGCG
CGATTGATGCGGATTTGCCGCGCGCCGAAGTGATTTTGCCGCGCAAAACG
GTGCTGGAACTGTTCAAACTGTTGAACAACCCCGACGATCCGATTCAAAT
CGAGCTGCTGGACAAGCAGGTGCGTTTCCAATGCAACGGCACGACCATCG
TCAGCAAGGTCATCGACGGCAAATTCCCCGATTTCAACCGCGTGATTCCT
TTGGACAACGACAAGATTTTCGTGTTGTCCCGTGCCGAACTTTTGGGCGC
GCTGGAACGTGTGTCCATTCTTGCCAACGAAAAATTCCGTGGCGCGCGCC
TGTTCCTGCAACCCGGCCTGTTGAGCGTCGTGTGCAGCAACAACGAGCAG
GAAGAAGCGCGCGAAGAAATCGAAATCGCCTATCAGGGCGGCGAACTCGA
AGTCGGTTTCAATATCGGCTATTTGATGGACGTGTTGCGCAACATCCATT
CCGACGATATGCAGCTTGCCTTCGGCGACGCCAACCGCTCGACGCTGTTT
ACCGTGCCGAACAATCCGAATTTCAAATATATTGTGATGCCGATGCGGAT
T


Los Alamos National Laboratory     
Operated by the University of California for the National Nuclear Security Administration,
of the US Department of Energy.     Copyright © 2001 UC | Disclaimer/Privacy