[English] 日本語
Yorodumi
- SASDEM9: anEcTFE: Escherichia coli anaerobic fatty acid beta-oxidation tri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDEM9
SampleanEcTFE: Escherichia coli anaerobic fatty acid beta-oxidation trifunctional enzyme complex
  • anaerobic Fatty acid oxidation complex subunit alpha (protein), anEcTFE-alpha, Escherichia coli (strain K12)
  • anaerobic Fatty acid oxidation complex subunit alpha (protein), anEcTFE-alpha, Escherichia coli (strain K12)
  • anaerobic Fatty acid oxidation complex subunit alpha (protein), anEcTFE-alpha, Escherichia coli (strain K12)
  • anaerobic Fatty acid oxidation complex subunit alpha (protein), anEcTFE-alpha, Escherichia coli (strain K12)
  • anaerobic 3-ketoacyl-CoA thiolase FadI beta subunit (protein), anEcTFE-beta, Escherichia coli (strain K12)
  • anaerobic 3-ketoacyl-CoA thiolase FadI beta subunit (protein), anEcTFE-beta, Escherichia coli (strain K12)
Function / homology
Function and homology information


fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / acetyl-CoA C-acetyltransferase activity ...fatty acid beta-oxidation, unsaturated, even number / fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / acetyl-CoA C-acyltransferase / acetyl-CoA C-acyltransferase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / acetyl-CoA C-acetyltransferase activity / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding / cytoplasm / cytosol
Similarity search - Function
Acetyl-CoA C-acyltransferase FadI / Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. ...Acetyl-CoA C-acyltransferase FadI / Fatty oxidation complex, alpha subunit FadJ / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Thiolase-like / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-ketoacyl-CoA thiolase FadI / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria)
CitationJournal: Biochem J / Year: 2019
Title: Complementary substrate specificity and distinct quaternary assembly of the aerobic and anaerobic β-oxidation trifunctional enzyme complexes.
Authors: Shiv K Sah-Teli / Mikko J Hynönen / Werner Schmitz / James A Geraets / Jani Seitsonen / Jan Skov Pedersen / Sarah J Butcher / Rik K Wierenga / Rajaram Venkatesan /
Abstract: The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, ...The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetramers in the octamer is different from the HsTFE octamer. These studies demonstrate that EcTFE and anEcTFE have complementary substrate specificities, allowing for complete degradation of long-chain enoyl-CoAs under aerobic conditions. The new data agree with the notion that anEcTFE and HsTFE are evolutionary closely related, whereas EcTFE belongs to a separate subfamily.
Contact author
  • shiv k. sah-teli (University of Oulu, Finland)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2749
Type: dummy / Radius of dummy atoms: 5.00 A / Symmetry: p1 / Chi-square value: 1.010 / P-value: 0.000235
Search similar-shape structures of this assembly by Omokage search (details)
Model #2750
Type: atomic
Comment: subunits and complex were modeled using swissmodel and coot respectively using 5zqz.pdb as referenc
Chi-square value: 3.501
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: anEcTFE: Escherichia coli anaerobic fatty acid beta-oxidation trifunctional enzyme complex
Specimen concentration: 3.5 mg/ml / Entity id: 1435 / 1436 / 1437 / 1438 / 1439 / 1440
BufferName: 50 mM Tris, 500 mM NaCl, 5% glycerol, 0.05% C12E9 (1-O-(n-Dodecyl)-nonaethyleneglycol), 2.5 mM DTT
pH: 8
Entity #1435Name: anEcTFE-alpha / Type: protein
Description: anaerobic Fatty acid oxidation complex subunit alpha
Formula weight: 77.071 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P77399
Sequence: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT ...Sequence:
MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT GKQLRAKQAL KLGLVDDVVP HSILLEAAVE LAKKERPSSR PLPVRERILA GPLGRALLFK MVGKKTEHKT QGNYPATERI LEVVETGLAQ GTSSGYDAEA RAFGELAMTP QSQALRSIFF ASTDVKKDPG SDAPPAPLNS VGILGGGLMG GGIAYVTACK AGIPVRIKDI NPQGINHALK YSWDQLEGKV RRRHLKASER DKQLALISGT TDYRGFAHRD LIIEAVFENL ELKQQMVAEV EQNCAAHTIF ASNTSSLPIG DIAAHATRPE QVIGLHFFSP VEKMPLVEII PHAGTSAQTI ATTVKLAKKQ GKTPIVVRDK AGFYVNRILA PYINEAIRML TQGERVEHID AALVKFGFPV GPIQLLDEVG IDTGTKIIPV LEAAYGERFS APANVVSSIL NDDRKGRKNG RGFYLYGQKG RKSKKQVDPA IYPLIGTQGQ GRISAPQVAE RCVMLMLNEA VRCVDEQVIR SVRDGDIGAV FGIGFPPFLG GPFRYIDSLG AGEVVAIMQR LATQYGSRFT PCERLVEMGA RGESFWKTTA TDLQ
Entity #1436Name: anEcTFE-alpha / Type: protein
Description: anaerobic Fatty acid oxidation complex subunit alpha
Formula weight: 77.071 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P77399
Sequence: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT ...Sequence:
MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT GKQLRAKQAL KLGLVDDVVP HSILLEAAVE LAKKERPSSR PLPVRERILA GPLGRALLFK MVGKKTEHKT QGNYPATERI LEVVETGLAQ GTSSGYDAEA RAFGELAMTP QSQALRSIFF ASTDVKKDPG SDAPPAPLNS VGILGGGLMG GGIAYVTACK AGIPVRIKDI NPQGINHALK YSWDQLEGKV RRRHLKASER DKQLALISGT TDYRGFAHRD LIIEAVFENL ELKQQMVAEV EQNCAAHTIF ASNTSSLPIG DIAAHATRPE QVIGLHFFSP VEKMPLVEII PHAGTSAQTI ATTVKLAKKQ GKTPIVVRDK AGFYVNRILA PYINEAIRML TQGERVEHID AALVKFGFPV GPIQLLDEVG IDTGTKIIPV LEAAYGERFS APANVVSSIL NDDRKGRKNG RGFYLYGQKG RKSKKQVDPA IYPLIGTQGQ GRISAPQVAE RCVMLMLNEA VRCVDEQVIR SVRDGDIGAV FGIGFPPFLG GPFRYIDSLG AGEVVAIMQR LATQYGSRFT PCERLVEMGA RGESFWKTTA TDLQ
Entity #1437Name: anEcTFE-alpha / Type: protein
Description: anaerobic Fatty acid oxidation complex subunit alpha
Formula weight: 77.071 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P77399
Sequence: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT ...Sequence:
MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT GKQLRAKQAL KLGLVDDVVP HSILLEAAVE LAKKERPSSR PLPVRERILA GPLGRALLFK MVGKKTEHKT QGNYPATERI LEVVETGLAQ GTSSGYDAEA RAFGELAMTP QSQALRSIFF ASTDVKKDPG SDAPPAPLNS VGILGGGLMG GGIAYVTACK AGIPVRIKDI NPQGINHALK YSWDQLEGKV RRRHLKASER DKQLALISGT TDYRGFAHRD LIIEAVFENL ELKQQMVAEV EQNCAAHTIF ASNTSSLPIG DIAAHATRPE QVIGLHFFSP VEKMPLVEII PHAGTSAQTI ATTVKLAKKQ GKTPIVVRDK AGFYVNRILA PYINEAIRML TQGERVEHID AALVKFGFPV GPIQLLDEVG IDTGTKIIPV LEAAYGERFS APANVVSSIL NDDRKGRKNG RGFYLYGQKG RKSKKQVDPA IYPLIGTQGQ GRISAPQVAE RCVMLMLNEA VRCVDEQVIR SVRDGDIGAV FGIGFPPFLG GPFRYIDSLG AGEVVAIMQR LATQYGSRFT PCERLVEMGA RGESFWKTTA TDLQ
Entity #1438Name: anEcTFE-alpha / Type: protein
Description: anaerobic Fatty acid oxidation complex subunit alpha
Formula weight: 77.071 / Num. of mol.: 1 / Source: Escherichia coli (strain K12) / References: UniProt: P77399
Sequence: MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT ...Sequence:
MEMTSAFTLN VRLDNIAVIT IDVPGEKMNT LKAEFASQVR AIIKQLRENK ELRGVVFVSA KPDNFIAGAD INMIGNCKTA QEAEALARQG QQLMAEIHAL PIQVIAAIHG ACLGGGLELA LACHGRVCTD DPKTVLGLPE VQLGLLPGSG GTQRLPRLIG VSTALEMILT GKQLRAKQAL KLGLVDDVVP HSILLEAAVE LAKKERPSSR PLPVRERILA GPLGRALLFK MVGKKTEHKT QGNYPATERI LEVVETGLAQ GTSSGYDAEA RAFGELAMTP QSQALRSIFF ASTDVKKDPG SDAPPAPLNS VGILGGGLMG GGIAYVTACK AGIPVRIKDI NPQGINHALK YSWDQLEGKV RRRHLKASER DKQLALISGT TDYRGFAHRD LIIEAVFENL ELKQQMVAEV EQNCAAHTIF ASNTSSLPIG DIAAHATRPE QVIGLHFFSP VEKMPLVEII PHAGTSAQTI ATTVKLAKKQ GKTPIVVRDK AGFYVNRILA PYINEAIRML TQGERVEHID AALVKFGFPV GPIQLLDEVG IDTGTKIIPV LEAAYGERFS APANVVSSIL NDDRKGRKNG RGFYLYGQKG RKSKKQVDPA IYPLIGTQGQ GRISAPQVAE RCVMLMLNEA VRCVDEQVIR SVRDGDIGAV FGIGFPPFLG GPFRYIDSLG AGEVVAIMQR LATQYGSRFT PCERLVEMGA RGESFWKTTA TDLQ
Entity #1439Name: anEcTFE-beta / Type: protein
Description: anaerobic 3-ketoacyl-CoA thiolase FadI beta subunit
Formula weight: 48.143 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P76503
Sequence: MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPNI AREIVLGTGM NVHTDAYSVS RACATSFQAV ANVAESLMAG TIRAGIAGGA DSSSVLPIGV SKKLARVLVD VNKARTMSQR ...Sequence:
MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPNI AREIVLGTGM NVHTDAYSVS RACATSFQAV ANVAESLMAG TIRAGIAGGA DSSSVLPIGV SKKLARVLVD VNKARTMSQR LKLFSRLRLR DLMPVPPAVA EYSTGLRMGD TAEQMAKTYG ITREQQDALA HRSHQRAAQA WSDGKLKEEV MTAFIPPYKQ PLVEDNNIRG NSSLADYAKL RPAFDRKHGT VTAANSTPLT DGAAAVILMT ESRAKELGLV PLGYLRSYAF TAIDVWQDML LGPAWSTPLA LERAGLTMSD LTLIDMHEAF AAQTLANIQL LGSERFAREA LGRAHATGEV DDSKFNVLGG SIAYGHPFAA TGARMITQTL HELRRRGGGF GLVTACAAGG LGAAMVLEAE
Entity #1440Name: anEcTFE-beta / Type: protein
Description: anaerobic 3-ketoacyl-CoA thiolase FadI beta subunit
Formula weight: 48.143 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P76503
Sequence: MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPNI AREIVLGTGM NVHTDAYSVS RACATSFQAV ANVAESLMAG TIRAGIAGGA DSSSVLPIGV SKKLARVLVD VNKARTMSQR ...Sequence:
MGSSHHHHHH SQDPMGQVLP LVTRQGDRIA IVSGLRTPFA RQATAFHGIP AVDLGKMVVG ELLARSEIPA EVIEQLVFGQ VVQMPEAPNI AREIVLGTGM NVHTDAYSVS RACATSFQAV ANVAESLMAG TIRAGIAGGA DSSSVLPIGV SKKLARVLVD VNKARTMSQR LKLFSRLRLR DLMPVPPAVA EYSTGLRMGD TAEQMAKTYG ITREQQDALA HRSHQRAAQA WSDGKLKEEV MTAFIPPYKQ PLVEDNNIRG NSSLADYAKL RPAFDRKHGT VTAANSTPLT DGAAAVILMT ESRAKELGLV PLGYLRSYAF TAIDVWQDML LGPAWSTPLA LERAGLTMSD LTLIDMHEAF AAQTLANIQL LGSERFAREA LGRAHATGEV DDSKFNVLGG SIAYGHPFAA TGARMITQTL HELRRRGGGF GLVTACAAGG LGAAMVLEAE

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 2.867 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: anEcTFE: Escherichia coli anaerobic fatty acid beta-oxidation trifunctional enzyme complex
Measurement date: Sep 22, 2015 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 1200 / Unit: 1/A /
MinMax
Q0.005 0.1711
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 264 /
MinMax
Q0.00504644 0.129032
P(R) point1 264
R0 195.7
Result
Type of curve: sec /
ExperimentalPorod
MW535 kDa535 kDa
Volume-856 nm3

P(R)GuinierGuinier error
Forward scattering, I058.74 58.9 0.14
Radius of gyration, Rg6.15 nm6.19 nm0.02

MinMax
D-19.57
Guinier point1 35

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more