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(-) Description

Title :  STRUCTURE OF A CYSTEINE DESULFURASE FROM ESCHERICHIA COLI AT 2.384 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) - 23 Nov 16  (Release) - 23 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.38
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, J. F. Quintana, A. Round, R. Campos-Oliva, M. Bruix, M. Coll I. Tunon, J. Jimenez-Barbero, M. C. Vega
Mechanism Of Sulfur Transfer Across Protein-Protein Interfaces: The Cysteine Desulfurase Model System
Acs Catalysis V. 6 3975 2016
PubMed: search  |  Reference-DOI: 10.1021/ACSCATAL.6B00360

(-) Compounds

Molecule 1 - L-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  (5, 17)

Asymmetric/Biological Unit (5, 17)
No.NameCountTypeFull Name
1CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
2GOL10Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
5TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:28 , ALA B:47 , THR B:273 , VAL B:276BINDING SITE FOR RESIDUE GOL B1402
02AC2SOFTWAREARG A:302 , PRO A:316 , GLN A:324 , ALA A:334 , VAL A:400 , GOL A:1406BINDING SITE FOR RESIDUE GOL A1402
03AC3SOFTWARETYR A:65 , ARG A:69 , TRP A:86 , HOH A:2034 , HOH A:2035BINDING SITE FOR RESIDUE GOL A1403
04AC4SOFTWAREALA A:63 , ARG A:64 , LYS A:71 , GLU A:287BINDING SITE FOR RESIDUE GOL A1404
05AC5SOFTWAREHIS A:338 , SER A:339 , HOH A:2130BINDING SITE FOR RESIDUE GOL A1405
06AC6SOFTWAREVAL A:400 , GOL A:1402 , HOH A:2116BINDING SITE FOR RESIDUE GOL A1406
07AC7SOFTWAREPHE A:4 , TRP A:300 , ARG A:319BINDING SITE FOR RESIDUE GOL A1407
08AC8SOFTWAREARG A:10 , TRP A:300 , THR A:381 , LYS A:382 , SER A:383BINDING SITE FOR RESIDUE PEG A1408
09AC9SOFTWAREALA A:26 , ALA A:27 , HIS A:119 , ASN A:171 , LYS A:222 , ARG A:353 , HIS A:357 , CSS A:358 , ARG A:373 , PLP A:1410 , LYS B:250BINDING SITE FOR RESIDUE TLA A1409
10BC1SOFTWARETHR 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 , TLA A:1409 , HOH A:2043 , HOH A:2152 , GLY B:272 , THR B:273BINDING SITE FOR RESIDUE PLP A1410
11BC2SOFTWARETYR B:65 , GLU B:66 , ALA B:68 , ARG B:69 , TRP B:86BINDING SITE FOR RESIDUE GOL B1403
12BC3SOFTWAREASP A:151 , ARG B:10 , THR B:381 , SER B:383BINDING SITE FOR RESIDUE GOL B1404
13BC4SOFTWAREHIS B:51 , ARG B:52 , PHE B:55 , PHE B:204 , ARG B:302 , GLN B:324 , HOH B:2132BINDING SITE FOR RESIDUE GOL B1405
14BC5SOFTWAREHIS B:119 , LYS B:222 , ARG B:353 , HIS B:357 , CSS B:358 , ARG B:373 , PLP B:1407 , HOH B:2147BINDING SITE FOR RESIDUE TLA B1406
15BC6SOFTWAREGLY A:272 , THR A:273 , THR B:90 , THR B:91 , HIS B:119 , ALA B:121 , ASP B:196 , ALA B:198 , GLN B:199 , SER B:219 , HIS B:221 , LYS B:222 , TLA B:1406 , HOH B:2052 , HOH B:2147BINDING SITE FOR RESIDUE PLP B1407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FT5)

(-) 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 5FT5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FT5)

(-) Exons   (0, 0)

(no "Exon" information available for 5FT5)

(-) 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:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               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
                 5ft5 A   1 MNVFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGNVHRSQFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHcAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLVD 401
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 
                                                                                                                                                                                                                                                                                                                                                                                               358-CSS                                       


Chain B from PDB  Type:PROTEIN  Length:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhee.........hhhhhhhhhhhhh.........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
                 5ft5 B   1 MNVFNPAQFRAQFPALQDAGVYLDSAATALKPEAVVEATQQFYSLSAGNVHRSQFAEAQRLTARYEAAREKVAQLLNAPDDKTIVWTRGTTESINMVAQCYARPRLQPGDEIIVSVAEHHANLVPWLMVAQQTGAKVVKLPLNAQRLPDVDLLPELITPRSRILALGQMSNVTGGCPDLARAITFAHSAGMVVMVDGAQGAVHFPADVQQLDIDFYAFSGHKLYGPTGIGVLYGKSELLEAMSPWLGGGKMVHEVSFDGFTTQSAPWKLEAGTPNVAGVIGLSAALEWLADYDINQAESWSRSLATLAEDALAKRPGFRSFRCQDSSLLAFDFAGVHHSDMVTLLAEYGIALRAGQHcAQPLLAELGVTGTLRASFAPYNTKSDVDALVNAVDRALELLVD 401
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400 
                                                                                                                                                                                                                                                                                                                                                                                               358-CSS
   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 5FT5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FT5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FT5)

(-) 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 ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        CSDA_ECOLI | Q46925: 4lw2 4lw4 5ft4 5ft6 5ft8

(-) Related Entries Specified in the PDB File

5ft4 STRUCTURE OF A CYSTEINE DESULFURASE FROM ESCHERICHIA COLI AT 1.996 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