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(-) Description

Title :  STRUCTURE OF SLR0077/SUFS, THE ESSENTIAL CYSTEINE DESULFURASE FROM SYNECHOCYSTIS PCC 6803
 
Authors :  B. Tirupati, J. L. Vey, C. L. Drennan, J. M. Bollinger Jr.
Date :  26 Apr 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plp-Binding Enzyme, Cysteine Desulfurase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Tirupati, J. L. Vey, C. L. Drennan, J. M. Bollinger Jr.
Kinetic And Structural Characterization Of Slr0077/Sufs, Th Essential Cysteine Desulfurase From Synechocystis Sp. Pcc 6803.
Biochemistry V. 43 12210 2004
PubMed-ID: 15379559  |  Reference-DOI: 10.1021/BI0491447

(-) Compounds

Molecule 1 - PROBABLE CYSTEINE DESULFURASE
    Chains: A, B
    EC Number: 2.8.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) STAR CELLS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CSD, SLR0077
    Organism Scientific: SYNECHOCYSTIS SP.
    Organism Taxid: 1143

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
12OS1Ligand/Ion3-N-OCTANOYLSUCROSE
2GOL2Ligand/IonGLYCEROL
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:151 , ASP A:152 , GLU A:153 , GLU A:155 , ARG A:328 , TYR A:330 , HIS A:377 , PHE A:380 , HOH A:620 , HOH A:655 , HOH A:680 , HOH A:790 , ASP B:152 , GLU B:153 , GLN B:154 , HOH B:657BINDING SITE FOR RESIDUE 2OS A 602
2AC2SOFTWAREASN A:98 , ALA A:99 , THR A:100 , HIS A:128 , VAL A:176 , ASN A:180 , ASP A:205 , CYS A:207 , GLN A:208 , SER A:228 , HIS A:230 , LYS A:231 , GOL A:603 , HOH A:660 , GLY B:281 , THR B:282BINDING SITE FOR RESIDUE PLP A 600
3AC3SOFTWAREGLY A:281 , THR A:282 , ASN B:98 , ALA B:99 , THR B:100 , HIS B:128 , VAL B:176 , ASN B:180 , ASP B:205 , CYS B:207 , GLN B:208 , SER B:228 , HIS B:230 , LYS B:231 , GOL B:604 , HOH B:670BINDING SITE FOR RESIDUE PLP B 601
4AC4SOFTWAREALA A:35 , ALA A:36 , HIS A:128 , ASN A:180 , GLN A:208 , ARG A:367 , HIS A:371 , CYS A:372 , ARG A:387 , PLP A:600BINDING SITE FOR RESIDUE GOL A 603
5AC5SOFTWAREALA B:35 , HIS B:128 , ASN B:180 , ARG B:387 , PLP B:601BINDING SITE FOR RESIDUE GOL B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T3I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:274 -Pro A:275
2Leu B:274 -Pro B:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T3I)

(-) Exons   (0, 0)

(no "Exon" information available for 1T3I)

(-) 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:406
 aligned with CSD_SYNY3 | Q55793 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:408
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406        
            CSD_SYNY3     7 PSLAATVRQDFPILNQEINGHPLVYLDNAATSQKPRAVLEKLMHYYENDNANVHRGAHQLSVRATDAYEAVRNKVAKFINARSPREIVYTRNATEAINLVAYSWGMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDEQESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAPTGIGFLYGKEEILEAMPPFFGGGEMIAEVFFDHFTTGELPHKFEAGTPAIAEAIALGAAVDYLTDLGMENIHNYEVELTHYLWQGLGQIPQLRLYGPNPKHGDRAALASFNVAGLHASDVATMVDQDGIAIRSGHHCTQPLHRLFDASGSARASLYFYNTKEEIDLFLQSLQATIRFFS 414
               SCOP domains d1t3ia_ A: Probable cysteine desulfurase SufS                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t3iA01 A:7-34,A:302-414    ------1t3iA02 A:41-301 Ty  pe I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                               1t3iA01 A:7-34,A:302-414 Aspartate Aminotransferase, domain 1                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh..hhhhh.ee..ee.ee.........hhhhhhhhhhhhhhh....--..hhhhhhhhhhhhhhhhhhh......hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeee........hhhhhhhhh......eeee..........hhhhhhhhhh.....eeee..........hhhhhh..eeeee.hhh......eeeee.h.hhh...........eeee....eee...hhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhh..eeee...........eeeeee...hhhhhhhhhhh..ee.......hhhhhhhh.....eeee.....hhhhhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t3i A   7 PSLAATVRQDFPILNQEINGHPLVYLDNAATSQKPRAVLEKLMHYYENDNANV--GAHQLSVRATDAYEAVRNKVAKFINARSPREIVYTRNATEAINLVAYSWGMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDEQESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAPTGIGFLYGKEEILEAMPPFFGGGEMIAEVFFDHFTTGELPHKFEAGTPAIAEAIALGAAVDYLTDLGMENIHNYEVELTHYLWQGLGQIPQLRLYGPNPKHGDRAALASFNVAGLHASDVATMVDQDGIAIRSGHHCTQPLHRLFDASGSARASLYFYNTKEEIDLFLQSLQATIRFFS 414
                                    16        26        36        46        56  |  |  66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406        
                                                                               59 62                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with CSD_SYNY3 | Q55793 from UniProtKB/Swiss-Prot  Length:420

    Alignment length:408
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406        
            CSD_SYNY3     7 PSLAATVRQDFPILNQEINGHPLVYLDNAATSQKPRAVLEKLMHYYENDNANVHRGAHQLSVRATDAYEAVRNKVAKFINARSPREIVYTRNATEAINLVAYSWGMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDEQESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAPTGIGFLYGKEEILEAMPPFFGGGEMIAEVFFDHFTTGELPHKFEAGTPAIAEAIALGAAVDYLTDLGMENIHNYEVELTHYLWQGLGQIPQLRLYGPNPKHGDRAALASFNVAGLHASDVATMVDQDGIAIRSGHHCTQPLHRLFDASGSARASLYFYNTKEEIDLFLQSLQATIRFFS 414
               SCOP domains d1t3ib_ B: Probable cysteine desulfurase SufS                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1t3iB01 B:7-34,B:302-414    ------1t3iB02 B:41-301 Ty   pe I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                              1t3iB01 B:7-34,B:302-414 Aspartate Aminotransferase, domain 1                                                     CATH domains
           Pfam domains (1) -----------------------Aminotran_5-1t3iB01 B:30-402                                                                                                                                                                                                                                                                                                                                                         ------------ Pfam domains (1)
           Pfam domains (2) -----------------------Aminotran_5-1t3iB02 B:30-402                                                                                                                                                                                                                                                                                                                                                         ------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh........ee.........hhhhhhhhhhhhhhh....---...hhhhhhhhhhhhhhhhh......hhh.eeee.hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeee........hhhhhhhhh...eeeeeee..........hhhhhhhhhh....eeeee..........hhhhhh..eeeee.hhh......eeeee.h.hhh...........eeee....eee...hhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeee...........eeeeee...hhhhhhhhhhh..ee.......hhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t3i B   7 PSLAATVRQDFPILNQEINGHPLVYLDNAATSQKPRAVLEKLMHYYENDNANV---AHQLSVRATDAYEAVRNKVAKFINARSPREIVYTRNATEAINLVAYSWGMNNLKAGDEIITTVMEHHSNLVPWQMVAAKTGAVLKFVQLDEQESFDLEHFKTLLSEKTKLVTVVHISNTLGCVNPAEEIAQLAHQAGAKVLVDACQSAPHYPLDVQLIDCDWLVASGHKMCAPTGIGFLYGKEEILEAMPPFFGGGEMIAEVFFDHFTTGELPHKFEAGTPAIAEAIALGAAVDYLTDLGMENIHNYEVELTHYLWQGLGQIPQLRLYGPNPKHGDRAALASFNVAGLHASDVATMVDQDGIAIRSGHHCTQPLHRLFDASGSARASLYFYNTKEEIDLFLQSLQATIRFFS 414
                                    16        26        36        46        56  |   | 66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406        
                                                                               59  63
   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, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CSD_SYNY3 | Q55793)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0031071    cysteine desulfurase activity    Catalysis of the reaction: L-cysteine + [enzyme]-cysteine = L-alanine + [enzyme]-S-sulfanylcysteine.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006534    cysteine metabolic process    The chemical reactions and pathways involving cysteine, 2-amino-3-mercaptopropanoic acid.

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