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Neisseria gonorrhoeae Search Results

Record: 1 of 1  
MiniMap IGR0518 IGR0519 IGR0521 IGR0515.1 IGR0517 IGR0515 IGR0520 IGR0516 IGR0512 IGR0514 IGR0513 NG0616 NG0621 NG0613 panD, - NG0620 NG0618 kdsA, - NG0619 eno, - NG0617 NG0615.1 plsC, - NG0611 rir2,nrdB, - NG0615 rir1,nrdA, - NG0614 NG0616 NG0621 NG0613 panD, - NG0620 NG0618 kdsA, - NG0619 eno, - NG0617 NG0615.1 plsC, - NG0611 rir2,nrdB, - NG0615 rir1,nrdA, - NG0614 NG0616 NG0613 panD, - NG0620 NG0618 kdsA, - NG0619 eno, - NG0617 NG0621 NG0615.1 plsC, - NG0611 rir2,nrdB, - NG0615 rir1,nrdA, - NG0614
* Calculated from Protein Sequence

Gene ID: NG0615

DNA Molecule Name:
1  

Genbank ID:


Gene Name:
rir2  nrdB  

Definition:
ribonucleoside diphosphate reductase I beta chain (ribonucleotide reductase 1) (B2 protein) (R2 protein)

Gene Start:
602880

Gene Stop:
604031

Gene Length:
1152

Molecular Weight*:
44042

pI*:
4.50

Net Charge*:
-24.31

EC:
1.17.4.1  

Functional Class:
Purines, pyrimidines, nucleosides, and nucleotides; 2'-Deoxyribonucleotide metabolism  

Pathway: pathway table
Purine metabolism
Pyrimidine metabolism

Secondary Evidence:
Salowe,S.P. and Stubbe,J. Cloning, overproduction, and purification of the B2 subunit of ribonucleoside-diphosphate reductase. J. Bacteriol. 165 (2): 363-366 (1986) [Medline: 86111594].

Nordlund,P., Sjoberg,B.M. and Eklund,H. Three-dimensional structure of the free radical protein of ribonucleotide reductase. Nature 345 (6276): 593-598 (1990) [Medline: 90272001].

Nordlund,P. and Eklund,H. Structure and function of the Escherichia coli ribonucleotide reductase protein R2. J. Mol. Biol. 232 (1): 123-164 (1993) [Medline: 93323110].

Logan,D.T., Su,X.D., Aberg,A., Regnstrom,K., Hajdu,J., Eklund,H. and Nordlund,P. Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at adinuclear iron site. Structure 4 (9): 1053-1064 (1996) [Medline: 96398694].

Eriksson,M., Uhlin,U., Ramaswamy,S., Ekberg,M., Regnstrom,K., Sjoberg,B.M. and Eklund,H. Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding. Structure 5 (8): 1077-1092 (1997) [Medline: 97454793].

Tong,W., Burdi,D., Riggs-Gelasco,P., Chen,S., Edmondson,D., Huynh,B.H., Stubbe,J., Han,S., Arvai,A. and Tainer,J. Characterization of Y122F R2 of Escherichia coli ribonucleotide reductase by time-resolved physical biochemical methods and X-raycrystallography. Biochemistry 37 (17): 5840-5848 (1998) [Medline: 98226619].

Logan,D.T., deMare,F., Persson,B.O., Slaby,A., Sjoberg,B.M. and Nordlund,P. Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for theoxygen-insertion step of hydroxylation reactions catalyzed bydiiron proteins. Biochemistry 37 (30): 10798-10807 (1998) [Medline: 98367522].

Comment:
From GenBANK (gi:132621): R2 catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides, precursors that are necessary for dna synthesis. R2 contains the tyrosyl radical required for catalysis. Catalytic activity: 2'-deoxyribonucleoside diphosphate + oxidized thioredoxin + H2O = ribonucleoside diphosphate + reduced thioredoxin, requiring a cofactor, 2 iron ions. This is the first reaction in the DNA replication pathway. R2 is a tetramer of two alpha and two beta chains. The B2 protein is a dimer of beta chains. E.coli produces two separate class I enzymes; this one is the functional enzyme during growth. This protein belongs to the ribonucleoside diphosphate reductase small chain family.

See also NG0614, ribonucleoside diphosphate reductase alpha chain.

Oklahoma ID: NGO.615

Blast Summary:  PSI-Blast Search
Numerous significant hits in gapped BLAST to ribonucleoside-diphosphate reductase 1, beta subunit, B2; e.g. residues 8-384 are 82% similar to AE005456 of E. coli.

Residues 1-384 are 98% similar to NMB1288, and residues 8-384 are 98% similar to NMA1498, both ribonucleoside-diphosphate reductases of N.meningitidis (11256406, 11256404).

COGS Summary:  COGS Search
BeTs to 11 clades of COG0208
COG name: Ribonucleotide reductase beta subunit
Functional Class:  F
The phylogenetic pattern of COG0208 is ----YQ-cEBRhujgp-linx
Number of proteins in this genome belonging to this COG is 1

Blocks Summary:  Blocks Search
***** IPB000358 (Ribonucleotide reductase) with a combined E-value of 1.6e-43.
    IPB000358A    40-94
    IPB000358B    115-140
    IPB000358C    218-258
    IPB000358D    286-296
    IPB000358E    355-365


ProDom Summary:  Protein Domain Search
Residues 344-384 are 80% similar to a (RIBONUCLEOTIDE REDUCTASE RIBONUCLEOSIDE-DIPHOSPHATE BETA) protein domain (PD013745) which is seen in RIR2_ECOLI.

Residues 211-343 are 75% similar to a (REDUCTASE RIBONUCLEOTIDE CHAIN) protein domain (PD000938) which is seen in RIR2_SALTY.

Residues 9-209 are 85% similar to a (RIBONUCLEOTIDE REDUCTASE) protein domain (PD013746) which is seen in RIR2_ECOLI.



Paralogs:  Local Blast Search


NG0615 has no significant similarity (blastp p-value < 1e-3) to any other gene in this genome.


Pfam Summary:  Pfam Search
Residues 23 to 347 (E-value = 8.6e-145) place NG0615 in the Ribonuc_red_sm family which is described as Ribonucleotide reductase, small chain (PF00268)

Structural Feature(s):
Feature Type  Start  Stop
coil-coil  
273  
300

PDB Hit:
pdb|1JPR|1JPR-A MN SUBSTITUTED RIBONUCLEOTIDE REDUCTASE R2 FROM 622.0 0e+00
pdb|1BIQ|1BIQ-B RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA 618.0 0e+00
pdb|1MRR|1MRR-A PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE 618.0 0e+00
pdb|1RNR|1RNR-A PROT

Gene Protein Sequence:
MSCEHLVMSYSTFPKTKNDALKEPMFFGQPVNVARYDQQKYEVFEKLIEK
QLSFFWRPEEIDVSRDRIDYANLPEHEKHIFISNLKYQTLLDSIQGRSPN
VALLPLVSIPELETWVETWSFSETIHSRSYTHIIRNIVNDPSVVFDDIVE
NEYITARAEDIACYYDDLIEYTQYYNLLGEGVHNVGGKPVTVSLRGLKKK
LYLCLMCVNVLEAIRFYVSFACSFAFAERELMEGNAKIIKLIARDEALHL
TGTQHMLNLMRSGVDDPEMAEIAAELQDECFQLFKKAAEQEKEWAAYLFK
DGSMIGLNKEILSQYVEYITNLRMQAVGLPAGFEGANQNPIPWINAWLSS
DNVQVAPQEVEISSYLIGQIDSEVNTDDLGDFEL

Gene Nucleotide Sequence:  Sequence Viewer
ATGTCCTGCGAACACCTAGTCATGTCATACAGCACCTTTCCCAAAACCAA
AAACGACGCGCTGAAAGAGCCGATGTTTTTCGGTCAGCCGGTAAATGTCG
CCCGTTATGACCAGCAGAAATACGAGGTATTTGAAAAACTGATTGAAAAA
CAATTGTCGTTTTTTTGGCGGCCGGAAGAAATCGACGTGTCGCGCGACCG
TATCGACTACGCCAACCTGCCCGAACACGAAAAACATATTTTCATCAGCA
ATCTGAAATATCAAACACTGCTCGATTCCATCCAAGGGCGCAGTCCGAAT
GTTGCCTTGCTGCCTTTGGTTTCGATTCCCGAGCTGGAAACTTGGGTTGA
AACGTGGAGCTTCAGCGAAACCATCCACTCGCGCAGCTATACCCACATCA
TCCGCAATATTGTGAATGATCCGTCGGTCGTGTTTGATGATATTGTCGAA
AACGAATACATTACCGCCCGCGCCGAAGACATTGCCTGCTATTATGATGA
TTTAATCGAATACACCCAATATTACAACCTGTTGGGCGAAGGGGTGCACA
ATGTCGGCGGAAAACCCGTTACTGTGTCTTTGCGCGGGTTGAAGAAAAAA
CTCTATCTCTGCCTGATGTGCGTCAATGTGTTGGAAGCCATCCGTTTCTA
CGTTTCATTTGCCTGCTCGTTTGCTTTTGCTGAGCGTGAGTTGATGGAAG
GCAACGCCAAAATCATCAAACTGATTGCCCGCGATGAAGCCCTGCACCTG
ACCGGCACGCAGCATATGCTTAATCTGATGCGTTCGGGTGTTGATGATCC
GGAAATGGCGGAAATTGCCGCCGAGTTGCAGGACGAATGTTTCCAACTCT
TCAAAAAAGCGGCGGAACAGGAAAAAGAATGGGCGGCATATTTGTTTAAA
GACGGTTCGATGATCGGTTTGAACAAAGAAATCTTATCCCAATACGTCGA
ATATATTACCAATCTGCGTATGCAGGCGGTGGGGCTGCCGGCCGGATTTG
AAGGCGCAAATCAAAACCCGATTCCGTGGATTAATGCGTGGCTGTCGTCC
GACAACGTACAGGTCGCGCCGCAGGAAGTGGAAATATCCTCTTATTTGAT
TGGTCAAATCGATTCTGAAGTGAATACGGATGACTTGGGCGATTTTGAGT
TG


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