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(-) Description

Title :  STRUCTURE OF A CYSTEINE DESULFURASE FROM ESCHERICHIA COLI AT 1.996 ANGSTROEM RESOLUTION
 
Authors :  F. J. Fernandez, A. Arda, M. Lopez-Estepa, J. Aranda, E. Penya-Soler, F J. F. Quintana, A. Round, R. Campos-Oliva, M. Bruix, M. Coll, I. Tunon, J. Jimenez-Barbero, M. C. Vega
Date :  11 Jan 16  (Deposition) - 21 Dec 16  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, L-Cysteine Desulfurase, Sulfur Acceptor, Transpersulfuration, Sulfur Trafficking (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. J. Fernandez, A. Arda, M. Lopez-Estepa, J. Aranda, E. Penya-Soler, F. Garces, A. Round, R. Campos-Oliva, M. Bruix, M. Coll, I. Tunon, J. Jimenez-Barbero, M. C. Vega
The Mechanism Of Sulfur Transfer Across Protein- Protein Interfaces: The Csd Model
Acs Catalysis V. 6 3975 2016
PubMed: search  |  Reference-DOI: 10.1021/ACSCATAL.6B00360

(-) Compounds

Molecule 1 - CYSTEINE DESULFURASE CSDA
    Chains: A, B
    EC Number: 2.8.1.7, 4.4.1.-, 4.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET3A
    Expression System Vector Type: PLASMID
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: CYSTEINE SULFINATE DESULFINASE, CSD, SELENOCYSTEINE LYASE, L-CYSTEINE DESULFURASE CSDA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2GOL6Ligand/IonGLYCEROL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:91 , HIS A:119 , ALA A:121 , ASN A:171 , ASP A:196 , ALA A:198 , GLN A:199 , SER A:219 , HIS A:221 , LYS A:222 , CIT A:1404 , HOH A:2112 , HOH A:2117 , HOH A:2300 , THR B:273BINDING SITE FOR RESIDUE PLP A 1401
02AC2SOFTWAREGLY A:272 , THR A:273 , HOH A:2222 , HOH A:2238 , THR 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 , CIT B:1406 , HOH B:2089BINDING SITE FOR RESIDUE PLP B 1401
03AC3SOFTWAREGLN B:263 , TRP B:267BINDING SITE FOR RESIDUE GOL B 1402
04AC4SOFTWAREPRO B:104 , HOH B:2095 , HOH B:2275BINDING SITE FOR RESIDUE GOL B 1403
05AC5SOFTWARETYR A:65 , ARG A:69 , TRP A:86 , TRP A:267 , HOH A:2089BINDING SITE FOR RESIDUE GOL A 1402
06AC6SOFTWAREGLN A:99 , ARG A:103 , TRP A:245 , HOH A:2215 , HOH A:2301 , GLN B:99 , ARG B:103 , GLN B:132BINDING SITE FOR RESIDUE GOL A 1403
07AC7SOFTWAREALA B:47 , THR B:62 , TYR B:65 , HOH B:2276 , HOH B:2277BINDING SITE FOR RESIDUE GOL B 1404
08AC8SOFTWARETYR B:65 , ARG B:69 , TRP B:86 , TRP B:267 , HOH B:2055 , HOH B:2199BINDING SITE FOR RESIDUE GOL B 1405
09AC9SOFTWAREALA A:26 , ALA A:27 , HIS A:119 , ASN A:171 , LYS A:222 , ARG A:353 , HIS A:357 , CYS A:358 , ARG A:373 , PLP A:1401 , HOH A:2045 , HOH A:2276 , HOH A:2300 , LYS B:250 , THR B:273BINDING SITE FOR RESIDUE CIT A 1404
10BC1SOFTWARELYS A:250 , THR A:273 , HOH A:2222 , ALA B:26 , ALA B:27 , HIS B:119 , ASN B:171 , LYS B:222 , ARG B:353 , HIS B:357 , CYS B:358 , ARG B:373 , PLP B:1401 , HOH B:2022 , HOH B:2249BINDING SITE FOR RESIDUE CIT B 1406
11BC2SOFTWAREASN B:5 , PRO B:6 , ALA B:7 , ARG B:10 , HOH B:2279 , HOH B:2280 , HOH B:2281BINDING SITE FOR RESIDUE CIT B 1407
12BC3SOFTWAREHIS B:337 , HIS B:338 , SER B:339 , ALA B:354 , GLY B:355 , GLY B:370 , THR B:371 , HOH B:2240 , HOH B:2283BINDING SITE FOR RESIDUE CIT B 1408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FT4)

(-) 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 5FT4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FT4)

(-) Exons   (0, 0)

(no "Exon" information available for 5FT4)

(-) 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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...hhhhhhhhhhhh.ee.......hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ft4 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..........eeeeehhhhhhhh.........eeeee..eeee...hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....eee.......eeeeee...hhhhhhhhhhhh.ee.......hhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ft4 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
   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  (0, 0)

(no "SCOP Domain" information available for 5FT4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FT4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FT4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:265 - Pro A:266   [ RasMol ]  
    Ala B:265 - Pro B:266   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CSDA_ECOLI | Q46925: 4lw2 4lw4 5ft5 5ft6 5ft8

(-) Related Entries Specified in the PDB File

5ft5 STRUCTURE OF A CYSTEINE DESULFURASE FROM ESCHERICHIA COLI AT 2.384 ANGSTROEM RESOLUTION
5ft6 STRUCTURE OF A CYSTEINE DESULFURASE FROM ESCHERICHIA COLI AT 2.050 ANGSTROEM RESOLUTION
5ft7 STRUCTURE OF A SULFUR ACCEPTOR FROM ESCHERICHIA COLI AT 2.40 ANGSTROEM RESOLUTION
5ft8 STRUCTURE OF A CYSTEINE DESULFURASE-SULFUR ACCEPTOR COMPLEX FROM ESCHERICHIA COLI AT 2.50 ANGSTROEM RESOLUTION