Modomics - A Database of RNA Modifications

ID Card:

Full name: Cysteine desulfurase IscS subfamily
Synonym: NuvC
GI: 67466100
Orf: b2530
COG: COG1104
UniProt: P0A6B7
Structures: | 1P3W | 3LMV |
Alpha Fold Predicted Structure: AF-P0A6B7-F1
Enzyme type: cysteine desulfurase


PDB Structures:


1P3W

Structure Description:

Title: X-ray crystal structure of E. coli IscS
Classification: LYASE
Technique: X-Ray Diffraction
Resolution: 2.1
R value free: 0.236
R value observed: 0.206
R value work: 0.206

Abstract of the PDB Structure's related Publication:

IscS is a widely distributed cysteine desulfurase that catalyzes the pyridoxal phosphate-dependent desulfuration of L-cysteine and plays a central role in the delivery of sulfur to a variety of metabolic pathways. We report the crystal structure of Escherichia coli IscS to a resolution of 2.1A. The crystals belong to the space group P2(1)2(1)2(1) and have unit cell dimensions a=73.70A, b=101.97A, c=108.62A (alpha=beta=gamma=90 degrees ). Molecular replacement with the Thermotoga maritima NifS model was used to determine phasing, and the IscS model was refined to an R=20.6% (R(free)=23.6%) with two molecules per asymmetric unit. The structure of E.coli IscS is similar to that of T.maritima NifS with nearly identical secondary structure and an overall backbone r.m.s. difference of 1.4A. However, in contrast to NifS a peptide segment containing the catalytic cysteine residue (Cys328) is partially ordered in the IscS structure. This segment of IscS (residues 323-335) forms a surface loop directed away from the active site pocket. Cys328 is positioned greater than 17A from the pyridoxal phosphate cofactor, suggesting that a large conformational change must occur during catalysis in order for Cys328 to participate in nucleophilic attack of a pyridoxal phosphate-bound cysteine substrate. Modeling suggests that rotation of this loop may allow movement of Cys328 to within approximately 3A of the pyridoxal phosphate cofactor.

Download RCSB-PDB Structures:

Pdb Files   1P3W.pdb   3LMV.pdb  
Pdbx/mmCIF Files   1P3W.cif   3LMV.cif  


Protein sequence:

MKLPIYLDYSATTPVDPRVAEKMMQFMTMDGTFGNPASRSHRFGWQAEEAVDIARNQIADLVGADPREIVFTSGATESDNLAIKGAANFYQKKGKHIITSKTEHKAVLDTCRQLEREGFEVTYLAPQRNGIIDLKELEAAMRDDTILVSIMHVNNEIGVVQDIAAIGEMCRARGIIYHVDATQSVGKLPIDLSQLKVDLMSFSGHKIYGPKGIGALYVRRKPRVRIEAQMHGGGHERGMRSGTLPVHQIVGMGEAYRIAKEEMATEMERLRGLRNRLWNGIKDIEEVYLNGDLEHGAPNILNVSFNYVEGESLIMALKDLAVSSGSACTSASLEPSYVLRALGLNDELAHSSIRFSLGRFTTEEEIDYTIELVRKSIGRLRDLSPLWEMYKQGVDLNSIEWAHH

Comments:

IscS is a widely distributed cysteine desulfurase that catalyzes the pyridoxal phosphate-dependent desulfuration of L-cysteine and plays a central role in the delivery of sulfur to a variety of metabolic pathways (Cupp-Vickery et al. 2003 ). Together with MnmA, it has been shown that IscS is required for in vitro 2-thiouridine biosynthesis in E.coli. Other cofactors of other enzymes involved in thio-modification of tRNA: MnmA (s2U34), MiaB (ms2 on i6A37), ThiI (s4U8), TtcA (s2C32), TtuA (s2U54). NifS is the homolog in yeast and plants (Kambampati and Lauhon 2003 ). NifS is the homolog in yeast and plants.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M K L P I Y L D Y S A T T P V D P R V A E K M M Q F M T M D G T F G N P A S R S H R F G W Q A E E A V D I A R N Q I A D L V G A D P R E I V F T S G A T E S D N L A I K G A A N F Y Q K K G K H I I T S K T E H K A V L D T C R Q L E R E G F E V T Y L A P Q R N G I I D L K E L E A A M R D D T I L V S I M H V N N E I G V V Q D I A A I G E M C R A R G I I Y H V D A T Q S V G K L P I D L S Q L K V D L M S F S G H K I Y G P K G I G A L Y V R R K P R V R I E A Q M H G G G H E R G M R S G T L P V H Q I V G M G E A Y R I A K E E M A T E M E R L R G L R N R L W N G I K D I E E V Y L N G D L E H G A P N I L N V S F N Y V E G E S L I M A L K D L A V S S G S A C T S A S L E P S Y V L R A L G L N D E L A H S S I R F S L G R F T T E E E I D Y T I E L V R K S I G R L R D L S P L W E M Y K Q G V D L N S I E W A H H
50100150200250300350400SequenceGHTBSN

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P0A6B7-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0A6B7-F1.cif  
DSSP Secondary Structures   P0A6B7.dssp  





Publications:

Links:

_PubMed_
_EcoCyc_