PANDIT+

KeywordFamilyClanGene   

Entry: Rieske (PF00355)

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Pfam summary

Description

Rieske [2Fe-2S] domain

The rieske domain has a [2Fe-2S] centre. Two conserved cysteines that one Fe ion while the other Fe ion is coordinated by two conserved histidines.
 
Literature1. Iwata S, Saynovits M, Link TA, Michel H Structure 1996;4:567-579.Structure of a water soluble fragment of the 'Rieske' iron- sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution. PUBMED:8736555
2. Huang JT, Struck F, Matzinger DF, Levings CS; Proc Natl Acad Sci U S A 1991;88:10716-10720.Functional analysis in yeast of cDNA coding for the mitochondrial Rieske iron-sulfur protein of higher plants. PUBMED:1961737
3. Brandt U, Yu L, Yu CA, Trumpower BL; J Biol Chem 1993;268:8387-8390.The mitochondrial targeting presequence of the Rieske iron-sulfur protein is processed in a single step after insertion into the cytochrome bc1 complex in mammals and retained as a subunit in the complex. PUBMED:8386158
 
 
InterPro entry IPR005806
 

Alignment
New Hampshire tree

The seed alignment for this family in the PANDIT database contains 160 aligned sequences:

  BENA_ACIAD/52-155   BNZC_PSEPU/1-94   BPHA3_PSES1/2-96   BPHA_BURCE/56-163   CBAA_COMTE/26-129   CBDA_BURCE/54-157   CHMO_ARATH/95-189   CHMO_SPIOL/119-216   HCAC_ECOLI/2-95   HCAE_ECOLI/42-143   NASE_BACSU/4-99   NDOA_PSEPU/3-96   NIR_EMENI/931-1036   O04127_MAIZE/19-120   O05935_PSEPU/43-146   O07070_BURCE/1-95   O07622_BACSU/417-509   O24841_ACIAD/6-103   O24846_ACIAD/2-95   O24847_ACIAD/25-126   O42346_XENLA/68-161   O44512_CAEEL/175-267   O52396_THETH/89-185   O52833_BORBR/39-142   O53311_MYCTU/52-146   O54095_STRCO/5-107   O66460_AQUAE/66-167   O69180_ALCEU/1-95   O69363_RHOER/37-138   O69365_RHOER/19-111   O69839_STRCO/423-513   O74998_PHANO/954-1059   O77266_DROME/16-109   O82822_PSEST/4-98   O85283_9SPHN/32-133   O85285_9SPHN/2-95   O85673_ACIAD/50-149   O85777_RHILV/4-98   O85843_SPHAR/37-137   O85959_SPHAR/38-137   O85964_SPHAR/38-139   O85966_SPHAR/45-146   O85986_SPHAR/40-142   O85989_SPHAR/58-160   O85991_SPHAR/3-97   O85993_SPHAR/44-144   O86899_9SPHN/42-140   O86905_9SPHN/56-155   O86907_9SPHN/3-96   O86909_9SPHN/63-164   O86913_9SPHN/67-168   More...

The full alignment for this family in the Pfam database contains 6543 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Novosphingobium aromaticivorans (8);   Pseudomonas putida (8);   Synechocystis sp. PCC 6803 (8);   Streptomyces coelicolor (7);   Arabidopsis thaliana (6);   Sphingomonas sp. (5);   Acinetobacter sp. ADP1 (5);   Pseudomonas aeruginosa (4);   Bacillus subtilis (3);   Burkholderia cepacia (3);   Chlamydomonas reinhardtii (3);   Rhodococcus erythropolis (3);   Escherichia coli K12 (3);   Pseudomonas stutzeri (3);   Sphingomonas sp. CB3 (2);   Thermotoga maritima (2);   Drosophila melanogaster (2);   Aeropyrum pernix (2);   Deinococcus radiodurans (2);   Mycobacterium tuberculosis (2);   Methylosulfonomonas methylovora (2);   Alcaligenes faecalis (2);   Comamonas testosteroni (2);   Rhodopseudomonas palustris (2);   Synechococcus elongatus (1);   Blastochloris viridis (1);   Zea mays (1);   Rhodococcus globerulus (1);   Brucella abortus (1);   Pseudomonas abietaniphila (1);   Rhodospirillum rubrum (1);   Rhodococcus sp. RHA1 (1);   Heliobacillus mobilis (1);   Nostoc sp. PCC 7906 (1);   Spinacia oleracea (1);   Anabaena sp. (1);   Xanthobacter autotrophicus Py2 (1);   Hebeloma cylindrosporum (1);   Homo sapiens (1);   Chlorobaculum thiosulfatiphilum (1);   Burkholderia xenovorans LB400 (1);   Pseudomonas pseudoalcaligenes (1);   Marchantia polymorpha (1);   Aquifex aeolicus (1);   Myxococcus fulvus (1);   Nostoc sp. PCC 7120 (1);   Pseudomonas sp. JR1 (1);   Chlamydomonas sp. HS-5 (1);   Burkholderia pyrrocinia (1);   Pseudomonas mendocina (1);   Phormidium laminosum (1);   More...

The full alignment covers 1094 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-20430.42-20430.420824-20430.420778-19885.6701-19839.976194

Tree Length  

3129.573129.571673129.571673129.571673129.57167

κ  

1.521.5190981.5190991.5359431.52052

ω-ratio  

ω=0.00908p0=0.999999 ~ ω0=0.009084
p1=1.00000000002876e-06 ~ ω1=1		p0=1 ~ ω0=0.009084
p1=0 ~ ω1=1
p2=0 ~ ω2=69.124549		ω~Β(0.553448,8.265977)p0=0.999397 ~ ω~Β(0.635372,46.542568)
p1=0.000603 ~ ω=35.067704

P-value for testing  
positive selection  

M1 vs M2: P-value=0.999954
domain classification: conserved		M7 vs M8: P-value=0
domain classification: positively selected

Positively selected sites - the underlined numbers denote the position in the AA sequence, while the number in brackets denote the estimated probability for having positive selection at that position. Only positions where the estimated probability for positive selection is ≥0.95 are shown.

   Model M8:

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

 -45485.44517-44613.39609

Mean ω-ratio  

ω = 0.2061ω = 0.02617

Coeff. of variation  
of ω-ratio  

 CVω = 1.65245CVω = 1.41355
 

Annotations

InteractionsThis domain has 10 known interactions:
PF00032; PF00033; PF00355; PF00384; PF00848; PF00866; PF01568; PF02167; PF07992; PF08802;
StructuresThis domain has 190 structures:
Notation: PDB_ID (PDB chain, PDB residues)
More...
Gene Ontologies
Biological Process
 oxidation reduction[GO:0055114]
Molecular Function
 electron carrier activity[GO:0009055]
 2 iron, 2 sulfur cluster binding[GO:0051537]
 oxidoreductase activity[GO:0016491]
KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Fructose and mannose metabolism [KEGG]
Starch and sucrose metabolism [KEGG]
Aminosugars metabolism [KEGG]
Pyruvate metabolism [KEGG]
Butanoate metabolism [KEGG]
Energy Metabolism
Oxidative phosphorylation [KEGG]
Photosynthesis [KEGG]
Methane metabolism [KEGG]
Nitrogen metabolism [KEGG]
Lipid Metabolism
Fatty acid metabolism [KEGG]
Biosynthesis of steroids [KEGG]
Bile acid biosynthesis [KEGG]
Androgen and estrogen metabolism [KEGG]
Arachidonic acid metabolism [KEGG]
Sphingolipid metabolism [KEGG]
Nucleotide Metabolism
Purine metabolism [KEGG]
Amino Acid Metabolism
Glycine, serine and threonine metabolism [KEGG]
Histidine metabolism [KEGG]
Tyrosine metabolism [KEGG]
Phenylalanine metabolism [KEGG]
Metabolism of Other Amino Acids
Glutathione metabolism [KEGG]
Glycan Biosynthesis and Metabolism
Other glycan degradation [KEGG]
Metabolism of Cofactors and Vitamins
Vitamin B6 metabolism [KEGG]
Lipoic acid metabolism [KEGG]
Biosynthesis of Secondary Metabolites
Limonene and pinene degradation [KEGG]
Carotenoid biosynthesis [KEGG]
Alkaloid biosynthesis I [KEGG]
Xenobiotics Biodegradation and Metabolism
Geraniol degradation [KEGG]
1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation [KEGG]
gamma-Hexachlorocyclohexane degradation [KEGG]
Benzoate degradation via hydroxylation [KEGG]
Bisphenol A degradation [KEGG]
Fluorobenzoate degradation [KEGG]
Biphenyl degradation [KEGG]
Toluene and xylene degradation [KEGG]
2,4-Dichlorobenzoate degradation [KEGG]
1- and 2-Methylnaphthalene degradation [KEGG]
Tetrachloroethene degradation [KEGG]
Naphthalene and anthracene degradation [KEGG]
1,4-Dichlorobenzene degradation [KEGG]
Fluorene degradation [KEGG]
Carbazole degradation [KEGG]
Benzoate degradation via CoA ligation [KEGG]
3-Chloroacrylic acid degradation [KEGG]
Styrene degradation [KEGG]
Genetic Information Processing
Replication and Repair
DNA replication [KEGG]
Base excision repair [KEGG]
Nucleotide excision repair [KEGG]
Mismatch repair [KEGG]
Environmental Information Processing
Signal Transduction
Two-component system [KEGG]
Notch signaling pathway [KEGG]
Cellular Processes
Cell Motility
Flagellar assembly [KEGG]
Cell Growth and Death
Cell cycle [KEGG]
Human Diseases
Neurodegenerative Diseases
Alzheimer's disease [KEGG]
Parkinson's disease [KEGG]
Huntington's disease [KEGG]
DisProt- disorder annotation inferred from homologous DisProt sequences
DP00019
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

none

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders
Links to OMIM - for human genes coding for sequences from full alignment
 
191327 (1)