SUPERFAMILY 1.75 HMM library and genome assignments server

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R1 subunit of ribonucleotide reductase, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   R1 subunit of ribonucleotide reductase, N-terminal domain [ 48167]
Superfamily:   R1 subunit of ribonucleotide reductase, N-terminal domain [ 48168]
Families:   R1 subunit of ribonucleotide reductase, N-terminal domain [ 48169]


Superfamily statistics
Genomes (2,741) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 3,372 22,231 8
Proteins 3,363 22,157 8


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Oxidoreductases0Least InformativeDirect
Enzyme Commission (EC)Acting on CH or CH(2) groups0InformativeDirect
Enzyme Commission (EC)With a disulfide as acceptor0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR008926 SSF48168 Protein matches
Abstract

The large subunit (R1) of ribonucleotide reductase (RNR), is an essential enzyme required for DNA replication and DNA repair. In both Escherichia coli and higher organisms, the enzyme consists of two non-identical subunits, a dimer of an 85-kDa protein, R1, and a dimer of a 45-kDa protein, R2. Both subunits are essential for RNR enzyme activity - R1 contains, in the substrate binding site, the reducing active cysteine pair and R2 provides a catalytically essential organic radical. R1 is able to bind and reduce the four common ribonucleoside diphosphates. Substrate specificity is determined by nucleoside triphosphates binding to a protein site different from the active site and acting as allosteric effectors. Thus the presence of ATP makes the enzyme reduce CDP and UDP, dGTP favours ADP reduction and dTTP favours GDP reduction. dATP is a general inhibitor. This provides a mechanism for a balanced enzymatic production of building blocks for DNA synthesis [PubMed10542051].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a R1 subunit of ribonucleotide reductase, N-terminal domain domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the R1 subunit of ribonucleotide reductase, N-terminal domain superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Enzyme Commission (EC) · Enzyme Commission (EC) · Internal database links ]