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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 :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Cysteine Desulfurase, Csda, Sufs, 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, C
    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

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2PLP3Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 , THR A:273 , HOH A:661 , HOH A:702BINDING SITE FOR RESIDUE PLP A 501
2AC2SOFTWAREALA A:26 , ALA A:27 , ASN A:171 , ARG A:353 , HIS A:357 , ARG A:373 , HOH A:688BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWARETHR B:90 , THR B:91 , HIS B:119 , ASN B:171 , ASP B:196 , ALA B:198 , GLN B:199 , SER B:219 , HIS B:221 , LYS B:222 , HOH B:616 , HOH B:662 , THR C:273 , HOH C:626BINDING SITE FOR RESIDUE PLP B 501
4AC4SOFTWAREALA B:26 , ALA B:27 , ASN B:171 , LYS B:222 , ARG B:353 , HIS B:357 , ARG B:373 , HOH B:640 , HOH B:692 , HOH B:913 , HOH B:956BINDING SITE FOR RESIDUE GOL B 502
5AC5SOFTWAREGLY B:272 , THR B:273 , THR C:90 , THR C:91 , HIS C:119 , ASN C:171 , ASP C:196 , ALA C:198 , GLN C:199 , SER C:219 , HIS C:221 , LYS C:222 , HOH C:618 , HOH C:764 , HOH C:890BINDING SITE FOR RESIDUE PLP C 501
6AC6SOFTWAREALA C:26 , ALA C:27 , ASN C:171 , ARG C:353 , HIS C:357 , ARG C:373 , HOH C:669 , HOH C:700BINDING SITE FOR RESIDUE GOL C 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LW2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala A:265 -Pro A:266
2Ala B:265 -Pro B:266
3Ala C:265 -Pro C:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LW2)

(-) Exons   (0, 0)

(no "Exon" information available for 4LW2)

(-) Sequences/Alignments

Asymmetric 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4lw2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...hhhhhhee.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhh..........eeeee.hhh......eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhh.ee.......hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw2 A   2 NVFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGNVHRSQFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHCAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLV 400
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391         


Chain B from PDB  Type:PROTEIN  Length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4lw2b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..hhhhhhee.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhh..........eeeee..........eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhh.ee.......hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw2 B   2 NVFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGNVHRSQFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHCAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLV 400
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391         


Chain C from PDB  Type:PROTEIN  Length:398
                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4lw2c_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhee.........hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhh.........eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..hhhhhh..........eeeee.hhh......eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhhhee.......hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lw2 C   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
   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  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LW2)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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    Ala A:265 - Pro A:266   [ RasMol ]  
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        CSDA_ECOLI | Q46925: 4lw4 5ft4 5ft5 5ft6 5ft8

(-) Related Entries Specified in the PDB File

4lw4