Genome Property Definition Page

Accession

GenProp0289

Name

class I (aerobic) ribonucleotide reductase

Type

SYSTEM

Description

Ribonucleotide reductases (RNRs) are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. The class I RNRs [1] consist of two subunits, alpha and beta (also known as the large and small subunbits, respectively). Class I RNRs generate the required radical (on tyrosine) via a non-heme iron cofactor which resides in the beta subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The most common gene symbols for these genes are NrdE (alpha) and NrdF (beta), althought the first characterized complex from E.coli (NrdAB) turns out to be one of a pair in gammaproteobacteria and the more divergent one at that. Where multiple class I enzymes exist in a single organism they are presumed to be under differential regulation. Note that earlier reports of a manganese-based class IV system related to class I in high GC gram positive species was proved to be spurious [2]. Electrons for this reduction are supplied by glutaredoxin-like (NrdH, in some species [3]), or flavodoxins specific to this system which are in turn reduced by oxygen via thioredoxin reductase. Detection of this component is not required to set the YES state because of incomplete knowledge of the various homologs involved. Certain class I RNRs are associated with a gene of unknown function (NrdI). NrdI shows up more frequently, but not exclusively in species with more than one class I RNR, so it may be involved in regulation in some way.

JCVI Role

2'-Deoxyribonucleotide metabolism

Parent Property

GenProp0287: ribonucleotide reduction

Literature References

[ 1 ]Stubbe J  Di-iron-tyrosyl radical ribonucleotide reductases.  Curr Opin Chem Biol 2003 Apr;7(2):183-8.  PMID 12714050
[ 2 ]Hogbom M, Huque Y, Sjoberg BM, Nordlund P  Crystal structure of the di-iron/radical protein of ribonucleotide reductase from Corynebacterium ammoniagenes.  Biochemistry 2002 Jan 29;41(4):1381-9.  PMID 11802741
[ 3 ]Stehr M, Schneider G, Aslund F, Holmgren A, Lindqvist Y  Structural basis for the thioredoxin-like activity profile of the glutaredoxin-like NrdH-redoxin from Escherichia coli.  J Biol Chem 2001 Sep 21;276(38):35836-41. Epub 2001 Jul 5.  PMID 11441020

Gene Ontology Term

GO:0009265: 2'-deoxyribonucleotide biosynthetic process (biological_process)

Components

Step Name	Step Num	Required	Evidence (Method)	Evidence Go Terms
aerobic RNR, alpha (large) chain	NrdA/E	YES	TIGR02506 (HMM): ribonucleoside-diphosphate reductase, alpha subunit TIGR02510 (HMM): ribonucleoside-diphosphate reductase, alpha chain	GO:0009265: 2'-deoxyribonucleotide biosynthetic process GO:0009265: 2'-deoxyribonucleotide biosynthetic process
aerobic RNR, beta (small) chain	NrdB/F	YES	PF00268 (HMM): ribonucleoside-diphosphate reductase, beta subunit	GO:0009265: 2'-deoxyribonucleotide biosynthetic process
Unknown function	NrdI	NO	TIGR00333 (HMM): nrdI protein	GO:0009265: 2'-deoxyribonucleotide biosynthetic process
redoxin, ribonucleotide-reductase related	redoxin	NO	TIGR02194 (HMM): glutaredoxin-like protein NrdH TIGR01754 (HMM): putative ribonucleotide reductase-associated flavodoxin	GO:0009265: 2'-deoxyribonucleotide biosynthetic process GO:0009265: 2'-deoxyribonucleotide biosynthetic process

Parent Properties

Accession	Name
GenProp0287	ribonucleotide reduction

Sibling Properties

Accession	Name
GenProp0290	class II (B12-dependent) ribonucleotide reductase
GenProp0291	class III (anaerobic) ribonucleotide reductase