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(-) Description

Title :  STRUCTURAL CHANGES DURING CYSTEINE DESULFURASE CSDA AND SULFUR-ACCEPTOR CSDE INTERACTIONS PROVIDE INSIGHT INTO THE TRANS-PERSULFURATION
 
Authors :  S. Kim, S. Y. Park
Date :  26 Jul 13  (Deposition) - 07 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cysteine Desulfurase, Csda, Sufe, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kim, S. Y. Park
Structural Changes During Cysteine Desulfurase Csda And Sulfur-Acceptor Csde Interactions Provide Insight Into The Trans-Persulfuration.
J. Biol. Chem. 2013
PubMed-ID: 23913692  |  Reference-DOI: 10.1074/JBC.M113.480277

(-) Compounds

Molecule 1 - CYSTEINE SULFINATE DESULFINASE
    Chains: A, B
    EC Number: 4.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2810, CSDA, JW2781, YGDJ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: CSD
 
Molecule 2 - CYSTEINE DESULFURATION PROTEIN CSDE
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CSDE, ECOK1_3187
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 714962
    Strain: IHE3034

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:90 , THR A:91 , HIS A:119 , ASN A:171 , ASP A:196 , ALA A:198 , GLN A:199 , SER A:219 , HIS A:221 , LYS A:222 , HOH A:602 , HOH A:640 , HOH A:781 , THR B:273BINDING SITE FOR RESIDUE PLP A 500
2AC2SOFTWAREGLY A:272 , THR A:273 , THR B:90 , THR B:91 , HIS B:119 , ALA B:121 , ASN B:171 , ASP B:196 , ALA B:198 , GLN B:199 , SER B:219 , HIS B:221 , LYS B:222 , HOH B:640 , HOH B:654 , HOH B:757BINDING SITE FOR RESIDUE PLP B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LW4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:265 -Pro A:266
2Ala B:265 -Pro B:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LW4)

(-) Exons   (0, 0)

(no "Exon" information available for 4LW4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:392
                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4lw4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhee.........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhh..........eeeee.hhh......eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhh.ee.eee...hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw4 A   3 VFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHCAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLV 400
                                    12        22        32        42     || 58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398  
                                                                        48|                                                                                                                                                                                                                                                                                                                                                         
                                                                         55                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lw4b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...ee.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhh..hhhhhh..eeeee.hhh......eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhh.ee.eee...hhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw4 B   3 VFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGNVHRSQFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHCAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLV 400
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392        


Chain C from PDB  Type:PROTEIN  Length:145
                                                                                                                                                                                 
               SCOP domains d4lw4c_ C: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhh..ee.......eeeeeee.....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw4 C   3 NPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV 147
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142     


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains d4lw4d_ D: automated matches                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhh..eeee...eeeeeeee.....eeeeeee.hhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw4 D   8 GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAK 145
                                    17        27        37        47        57  ||    68        78        88        98       108       118       128       138       
                                                                               60|                                                                                   
                                                                                62
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LW4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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        CSDA_ECOLI | Q46925: 4lw2 5ft4 5ft5 5ft6 5ft8

(-) Related Entries Specified in the PDB File

4lw2 CYSTEINE DESULFURASE CSDA