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- SASDDB3: Human mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp het... -

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Basic information

Entry
Database: SASBDB / ID: SASDDB3
SampleHuman mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp heterodimer complex)
  • Cysteine desulfurase, mitochondrial (protein), NFS1, Homo sapiens
  • LYR motif-containing protein 4 (protein), ISD11, Homo sapiens
  • Acyl carrier protein (protein), Escherichia coli (strain K12)
Function / homology
Function and homology information


molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity ...molybdopterin cofactor metabolic process / Molybdenum cofactor biosynthesis / L-cysteine desulfurase complex / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / sulfur carrier activity / Complex III assembly / Maturation of TCA enzymes and regulation of TCA cycle / cysteine desulfurase / cysteine desulfurase activity / Mo-molybdopterin cofactor biosynthetic process / iron-sulfur cluster assembly complex / mitochondrial [2Fe-2S] assembly complex / [2Fe-2S] cluster assembly / lipid A biosynthetic process / iron-sulfur cluster assembly / lipid biosynthetic process / acyl binding / acyl carrier activity / iron-sulfur cluster binding / phosphopantetheine binding / fatty acid biosynthetic process / pyridoxal phosphate binding / nuclear body / mitochondrial matrix / response to xenobiotic stimulus / lipid binding / centrosome / structural molecule activity / protein homodimerization activity / mitochondrion / nucleoplasm / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
LYRM4, LYR domain / : / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) ...LYRM4, LYR domain / : / Cysteine desulfurase IscS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Pyridoxal phosphate-dependent transferase, small domain / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Acyl carrier protein / LYR motif-containing protein 4 / Cysteine desulfurase
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (strain K12) (bacteria)
CitationJournal: Structure / Year: 2018
Title: Architectural Features of Human Mitochondrial Cysteine Desulfurase Complexes from Crosslinking Mass Spectrometry and Small-Angle X-Ray Scattering.
Authors: Kai Cai / Ronnie O Frederick / Hesam Dashti / John L Markley /
Abstract: Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for ...Cysteine desulfurase plays a central role in mitochondrial iron-sulfur cluster biogenesis by generating sulfur through the conversion of L-cysteine to L-alanine and by serving as the platform for assembling other components of the biosynthetic machinery, including ISCU, frataxin, and ferredoxin. The human mitochondrial cysteine desulfurase complex consists of two copies each of NFS1, ISD11, and acyl carrier protein. We describe results from chemical crosslinking coupled with tandem mass spectrometry and small-angle X-ray scattering studies that are consistent with a closed NFS1 dimer rather than an open one for both the cysteine desulfurase-ISCU and cysteine desulfurase-ISCU-frataxin complexes. We present a structural model for the cysteine desulfurase-ISCU-frataxin complex derived from chemical crosslinking restraints in conjunction with the recent crystal structure of the cysteine desulfurase-ISCU-zinc complex and distance constraints from nuclear magnetic resonance.
Contact author
  • Kai Cai (University of Wisconsin-Madison, Madison, WI, USA)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1774
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.925444 / P-value: 0.253126
Search similar-shape structures of this assembly by Omokage search (details)
Model #1775
Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 2.617924
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Human mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp heterodimer complex)
Specimen concentration: 2.00-10.00 / Entity id: 958 / 959 / 960
BufferName: 20 mM HEPES, 150 mM NaCl, 5 mM TCEP / pH: 7.5 / Comment: HNT Buffer
Entity #958Name: NFS1 / Type: protein / Description: Cysteine desulfurase, mitochondrial / Formula weight: 44.913 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9Y697
Sequence: GPVLRPLYMD VQATTPLDPR VLDAMLPYLI NYYGNPHSRT HAYGWESEAA MERARQQVAS LIGADPREII FTSGATESNN IAIKGVARFY RSRKKHLITT QTEHKCVLDS CRSLEAEGFQ VTYLPVQKSG IIDLKELEAA IQPDTSLVSV MTVNNEIGVK QPIAEIGRIC ...Sequence:
GPVLRPLYMD VQATTPLDPR VLDAMLPYLI NYYGNPHSRT HAYGWESEAA MERARQQVAS LIGADPREII FTSGATESNN IAIKGVARFY RSRKKHLITT QTEHKCVLDS CRSLEAEGFQ VTYLPVQKSG IIDLKELEAA IQPDTSLVSV MTVNNEIGVK QPIAEIGRIC SSRKVYFHTD AAQAVGKIPL DVNDMKIDLM SISGHKIYGP KGVGAIYIRR RPRVRVEALQ SGGGQERGMR SGTVPTPLVV GLGAACEVAQ QEMEYDHKRI SKLSERLIQN IMKSLPDVVM NGDPKHHYPG CINLSFAYVE GESLLMALKD VALSSGSACT SASLEPSYVL RAIGTDEDLA HSSIRFGIGR FTTEEEVDYT VEKCIQHVKR LREMSPLWEM VQDGIDLKSI KWTQH
Entity #959Name: ISD11 / Type: protein / Description: LYR motif-containing protein 4 / Formula weight: 11.581 / Num. of mol.: 2 / Source: Homo sapiens / References: UniProt: Q9HD34
Sequence:
MAASSRAQVL SLYRAMLRES KRFSAYNYRT YAVRRIRDAF RENKNVKDPV EIQTLVNKAK RDLGVIRRQV HIGQLYSTDK LIIENRDMPR THHHHHH
Entity #960Type: protein / Description: Acyl carrier protein / Formula weight: 11.5 / Num. of mol.: 2 / Source: Escherichia coli (strain K12) / References: UniProt: P0A6A8
Sequence:
PspP0A6A8A CPECOLIAcy lcarrierpr oteinOSEsc herichiaco li(strainK12)GNacpPP E1SV2MSTIE ERVKKIIGEQ LGVKQEEVTN NASFVEDLGA DSLDTVELVM ALEEEFDTEI PDEEAEKITT VQAAIDYING HQA

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Experimental information

BeamInstrument name: NMRFAM Bruker Nanostar / City: Madison, WI / 国: USA / Type of source: X-ray in house / Wavelength: 0.15418 Å / Dist. spec. to detc.: 1 mm
DetectorName: VÅNTEC-2000 / Type: MikroGap / Pixsize x: 200 mm
Scan
Title: Human mitochondrial cysteine desulfurase (NFS1, ISD11 and Acp heterodimer complex)
Measurement date: May 22, 2017 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 3600 sec. / Number of frames: 4 / Unit: 1/A /
MinMax
Q0 0.256
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 152 /
MinMax
Q0.0128 0.226
P(R) point6 157
R0 118.3
Result
Type of curve: single_conc
Comments: Solution SAXS study the human mitochondrial cysteine desulfurase, which consists of three components: NFS1, ISD11 and Acp and forms a homodimer.
ExperimentalPorod
MW125 kDa-
Volume-203.5 nm3

P(R)GuinierGuinier errorP(R) error
Forward scattering, I0906.7 931.8 8.7 -
Radius of gyration, Rg3.65 nm3.7 nm0.46 0.05

MinMaxError
D-11.83 0.5
Guinier point12 26 -

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