Protein Family Models

This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB) . Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo [1]. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain [2]. [1]. 26190574. An Unexpected Duo: Rubredoxin Binds Nine TPR Motifs to Form. LapB, an Essential Regulator of Lipopolysaccharide Synthesis.. Prince C, Jia Z;. Structure. 2015;23:1500-1506.. [2]. 28581365. Fine Epitope Mapping of Monoclonal Antibodies to the DNA Repair. Protein, RadA.. Stuart MK, Hudman DA, Nachtrab SN, Hiatt JL, Seo J, Pullen SJ,. Sargentini NJ;. Monoclon Antib Immunodiagn Immunother. 2017;36:83-94. (from Pfam)

Date:

2024-08-14

This AAA domain is found in a wide variety of presumed DNA repair proteins. (from Pfam)

Date:

2024-08-14

Date:

2024-08-14

This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria [1]. [1]. 10064581. Physical interactions among circadian clock proteins KaiA, KaiB. and KaiC in cyanobacteria.. Iwasaki H, Taniguchi Y, Ishiura M, Kondo T;. EMBO J 1999;18:1137-1145. (from Pfam)

Date:

2024-08-14

The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops. [1]. 12208506. Domain structure and ATP-induced conformational changes in. Escherichia coli protease Lon revealed by limited proteolysis. and autolysis.. Vasilyeva OV, Kolygo KB, Leonova YF, Potapenko NA, Ovchinnikova. TV;. FEBS Lett 2002;526:66-70. (from Pfam)

Date:

2024-08-14

The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. (from Pfam)

Date:

2024-08-14

DNA repair protein RadA is responsible for the stabilization or processing of branched DNA molecules

Date:

2024-05-10

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

Gene:

radA

Date:

2024-05-30