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(-) Description

Title :  CRYSTAL STRUCTURE OF PLP-BOUND E. COLI SUFS (CYSTEINE PERSULFIDE INTERMEDIATE) IN SPACE GROUP P21
 
Authors :  M. A. Arbing, A. Shin, C. W. Koo, A. Medrano-Soto, D. Eisenberg
Date :  20 Aug 15  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Desulfurase, Pyridoxal 5'-Phosphate (Plp), Nifs Protein Family, Protein Binding, Transferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Arbing, A. Shin, C. W. Koo, A. Medrano-Soto, D. Eisenberg
Crystal Structure Of Plp-Bound E. Coli Sufs (Cysteine Persulfide Intermediate) In Space Group P21
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CYSTEINE DESULFURASE
    Chains: A, B
    EC Number: 2.8.1.7, 4.4.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMAPLE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SUFS, CSDB, YNHB, B1680, JW1670
    Organism Scientific: ESCHERICHIA COLI DH5[ALPHA]
    Organism Taxid: 668369
    Strain: DH5[ALPHA]
    Synonym: SELENOCYSTEINE BETA-LYASE, SCL, SELENOCYSTEINE LYASE, SELENOCYSTEINE REDUCTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2CSS2Mod. Amino AcidS-MERCAPTOCYSTEINE
3CYS1Mod. Amino AcidCYSTEINE
4EDO2Ligand/Ion1,2-ETHANEDIOL
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:94 , THR A:95 , HIS A:123 , ASN A:175 , ASP A:200 , ALA A:202 , GLN A:203 , SER A:223 , HIS A:225 , HOH A:637 , GLY B:277 , THR B:278binding site for residue PLP A 501
2AC2SOFTWAREASP A:211binding site for residue EDO A 502
3AC3SOFTWAREGLY A:277 , THR A:278 , THR B:94 , THR B:95 , HIS B:123 , ALA B:125 , ASN B:175 , ASP B:200 , ALA B:202 , GLN B:203 , SER B:223 , HIS B:225 , CIT B:503 , HOH B:657 , HOH B:666binding site for residue PLP B 501
4AC4SOFTWAREHIS A:55 , THR A:278 , HIS B:123 , ASN B:175 , CSS B:364 , ARG B:379 , PLP B:501 , HOH B:612binding site for residue CIT B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DB5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:270 -Pro A:271
2Ala B:270 -Pro B:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DB5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DB5)

(-) Exons   (0, 0)

(no "Exon" information available for 5DB5)

(-) 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:404
                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.ee..ee.ee.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..........hhhhhh..eeeee..........eeeeehhhhhh...........eeee.....eee...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee...hhhhhhhhhhhh.ee.......hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5db5 A   3 FSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEGGGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNNIAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHcAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLLG 406
                                    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       402    
                                                                                                                                                                                                                                                                                                                                                                                                   364-CSS                                      


Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.ee..ee.ee.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhhhh..eeeee..........hhhhhh..eeeee..........eeeeehhhhhh...........eeee.....eee...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee...hhhhhhhhhhhh.ee.......hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5db5 B   2 IFSVDKVRADFPVLSREVNGLPLAYLDSAASAQKPSQVIDAEAEFYRHGYAAVHRGIHTLSAQATEKMENVRKRASLFINARSAEELVFVRGTTEGINLVANSWGNSNVRAGDNIIISQMEHHANIVPWQMLCARVGAELRVIPLNPDGTLQLETLPTLFDEKTRLLAITHVSNVLGTENPLAEMITLAHQHGAKVLVDGAQAVMHHPVDVQALDCDFYVFSGHKLYGPTGIGILYVKEALLQEMPPWEGGGSMIATVSLSEGTTWTKAPWRFEAGTPNTGGIIGLGAALEYVSALGLNNIAEYEQNLMHYALSQLESVPDLTLYGPQNRLGVIAFNLGKHHAYDVGSFLDNYGIAVRTGHHcAMPLMAYYNVPAMCRASLAMYNTHEEVDRLVTGLQRIHRLLG 406
                                    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       401     
                                                                                                                                                                                                                                                                                                                                                                                                    364-CSS
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  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 5DB5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DB5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DB5)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:270 - Pro A:271   [ RasMol ]  
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 Related Entries

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UniProtKB/Swiss-Prot
        SUFS_ECOLI | P77444: 1c0n 1i29 1jf9 1kmj 1kmk

(-) Related Entries Specified in the PDB File

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