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(-) Description

Title :  STRUCTURE OF A CATALYTICALLY INACTIVE MUTANT (K223A) OF C-DES WITH A SUBSTRATE (CYSTINE) LINKED TO THE CO-FACTOR
 
Authors :  J. T. Kaiser, S. Bruno, T. Clausen, R. Huber, F. Schiaretti, A. Mozzarel D. Kessler
Date :  25 Oct 02  (Deposition) - 21 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inactive Mutant, Substrate Complex, Fe-S Cluster Synthesis, Nifs- Like, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. T. Kaiser, S. Bruno, T. Clausen, R. Huber, F. Schiaretti, A. Mozzarelli, D. Kessler
Snapshots Of The Cystine Lyase "C-Des" During Catalysis: Studies In Solution And In The Crystalline State
J. Biol. Chem. V. 278 357 2003
PubMed-ID: 12386155  |  Reference-DOI: 10.1074/JBC.M209862200

(-) Compounds

Molecule 1 - L-CYSTEINE/CYSTINE LYASE C-DES
    Chains: A, B
    EC Number: 4.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSA15-PUC19
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C-DES
    Mutation: YES
    Organism Scientific: SYNECHOCYSTIS SP. PCC 6714
    Organism Taxid: 1147

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CYS4Mod. Amino AcidCYSTEINE
2K2Ligand/IonPOTASSIUM ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:316 , ASN A:317 , LEU A:319 , VAL A:322BINDING SITE FOR RESIDUE K A 1001
2AC2SOFTWARELEU B:316 , ASN B:317 , LEU B:319 , VAL B:322 , HOH B:3109BINDING SITE FOR RESIDUE K B 1002
3AC3SOFTWAREASN A:87 , VAL A:88 , THR A:89 , HIS A:114 , SER A:164 , TRP A:168 , ASP A:197 , ALA A:199 , GLN A:200 , HIS A:222 , CYS A:2002 , TRP B:251 , ALA B:275 , THR B:276BINDING SITE FOR RESIDUE PLP A 2001
4AC4SOFTWAREGLY A:26 , GLY A:27 , TRP A:168 , GLN A:200 , ARG A:360 , ARG A:369 , PLP A:2001 , CYS A:2003BINDING SITE FOR RESIDUE CYS A 2002
5AC5SOFTWAREHIS A:114 , TRP A:168 , ARG A:360 , CYS A:2002 , TRP B:251BINDING SITE FOR RESIDUE CYS A 2003
6AC6SOFTWARETRP A:251 , ALA A:275 , THR A:276 , ASN B:87 , VAL B:88 , THR B:89 , HIS B:114 , TRP B:168 , ASP B:197 , ALA B:199 , GLN B:200 , HIS B:222 , CYS B:3002BINDING SITE FOR RESIDUE PLP B 3001
7AC7SOFTWARECYS A:3003 , GLY B:26 , GLY B:27 , HIS B:114 , TRP B:168 , GLN B:200 , ARG B:360 , ARG B:369 , PLP B:3001BINDING SITE FOR RESIDUE CYS B 3002
8AC8SOFTWAREPHE A:52 , TRP A:251 , HOH A:3332 , ARG B:360 , CYS B:3002 , HOH B:3160 , HOH B:3202BINDING SITE FOR RESIDUE CYS A 3003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N31)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:50 -Pro A:51
2Asp A:364 -Pro A:365
3Gly B:50 -Pro B:51
4Asp B:364 -Pro B:365

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N31)

(-) Exons   (0, 0)

(no "Exon" information available for 1N31)

(-) 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:386
 aligned with Q9ZHG9_SYNY4 | Q9ZHG9 from UniProtKB/TrEMBL  Length:393

    Alignment length:386
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      
         Q9ZHG9_SYNY4     8 IPDRHQFPGLANKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGLDWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGDAAAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQGNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWFAGPAGVGGLYIHGDCLGEINPTYVGWRSITYGAKGEPTGWAEGGKRFEVATSAYPQYAGLLAALQLHQRQGTAEERYQAICQRSEFLWRGLNQLPHVHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRTIADPDCIRACCHYITDEEEINHLLARLADFGP 393
               SCOP domains d1n31a_ A: Cystine C-S lyase C-des                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----1n31A01            1n31A02 A:32-295 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                    1n31A01 A:13-31,A:296-391 Aspartate Aminotransferase, domain 1                                  -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.hhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee.hhhhh...hhhhhhhh.....eeeeeee..........hhhhhhhhhhhh......eeeee..................eeeee...........eeeee...hhhhh.........eee.....eeee.hhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eee.........eeeeee....hhhhhhhhhhhh.ee.eee....eeeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n31 A   8 TPDRHQFPGLANKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGLDWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGDAAAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQGNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHAWFAGPAGVGGLYIHGDCLGEINPTYVGWRSITYGAKGEPTGWAEGGKRFEVATSAYPQYAGLLAALQLHQRQGTAEERYQAICQRSEFLWRGLNQLPHVHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRTIADPDCIRACCHYITDEEEINHLLARLADFGP 393
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      


Chain B from PDB  Type:PROTEIN  Length:386
 aligned with Q9ZHG9_SYNY4 | Q9ZHG9 from UniProtKB/TrEMBL  Length:393

    Alignment length:386
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387      
         Q9ZHG9_SYNY4     8 IPDRHQFPGLANKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGLDWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGDAAAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQGNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHKWFAGPAGVGGLYIHGDCLGEINPTYVGWRSITYGAKGEPTGWAEGGKRFEVATSAYPQYAGLLAALQLHQRQGTAEERYQAICQRSEFLWRGLNQLPHVHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRTIADPDCIRACCHYITDEEEINHLLARLADFGP 393
               SCOP domains d1n31b_ B: Cystine C-S lyase C-des                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -----1n31B01            1n31B02 B:32-295 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                    1n31B01 B:13-31,B:296-391 Aspartate Aminotransferase, domain 1                                  -- CATH domains
           Pfam domains (1) -------------Aminotran_5-1n31B01 B:21-384                                                                                                                                                                                                                                                                                                                                                --------- Pfam domains (1)
           Pfam domains (2) -------------Aminotran_5-1n31B02 B:21-384                                                                                                                                                                                                                                                                                                                                                --------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh..ee.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee.hhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhhh.eeeee.hhhhh...hhhhhhhh.....eeeeeee..........hhhhhhhhhhhh......eeeee..................eeeee...........eeeee...hhhhh.........eee.....eeee.hhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eee.........eeeeee....hhhhhhhhhhhh.ee.eee....eeeee.....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n31 B   8 TPDRHQFPGLANKTYFNFGGQGILPTVALEAITAMYGYLQENGPFSIAANQHIQQLIAQLRQALAETFNVDPNTITITDNVTTGCDIVLWGLDWHQGDEILLTDCEHPGIIAIVQAIAARFGITYRFFPVAATLNQGDAAAVLANHLGPKTRLVILSHLLWNTGQVLPLAEIMAVCRRHQGNYPVRVLVDGAQSAGSLPLDFSRLEVDYYAFTGHAWFAGPAGVGGLYIHGDCLGEINPTYVGWRSITYGAKGEPTGWAEGGKRFEVATSAYPQYAGLLAALQLHQRQGTAEERYQAICQRSEFLWRGLNQLPHVHCLATSAPQAGLVSFTVDSPLGHRAIVQKLEEQRIYLRTIADPDCIRACCHYITDEEEINHLLARLADFGP 393
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387
   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  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9ZHG9_SYNY4 | Q9ZHG9)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

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  1n31
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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZHG9_SYNY4 | Q9ZHG9: 1elq 1elu 1n2t

(-) Related Entries Specified in the PDB File

1elq 1elu 1n2t