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(-) Description

Title :  PMP BOUND FORM OF SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE OBTAINED AFTER CO-CRYSTALLIZATION WITH L-CYCLOSERINE
 
Authors :  S. R. Bharath, B. Shveta, K. H. Rajesh, H. S. Savithri, M. R. N. Murthy
Date :  11 Jan 12  (Deposition) - 30 May 12  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fold Type Ii Plp-Dependent Enzyme, Tryptophan Synthase Beta Subunit Like Family, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Bharath, S. Bisht, R. K. Harijan, H. S. Savithri, M. R. N. Murthy
Structural And Mutational Studies On Substrate Specificity And Catalysis Of Salmonella Typhimurium D-Cysteine Desulfhydrase.
Plos One V. 7 36267 2012
PubMed-ID: 22574144  |  Reference-DOI: 10.1371/JOURNAL.PONE.0036267

(-) Compounds

Molecule 1 - D-CYSTEINE DESULFHYDRASE
    Chains: A, B, C, D
    EC Number: 4.4.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21(DE3)ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DCYD, STM1953
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 90371

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2PMP4Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE
2PMP2Ligand/Ion4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:30 , LEU A:31 , HOH A:727BINDING SITE FOR RESIDUE BEN A 401
2AC2SOFTWAREASN A:50 , LYS A:51 , LYS A:54 , ASN A:79 , GLY A:194 , SER A:195 , ALA A:196 , GLY A:197 , THR A:198 , TYR A:287 , THR A:315 , GLY A:316 , GLY A:317 , HOH A:507 , HOH A:645BINDING SITE FOR RESIDUE PMP A 402
3AC3SOFTWAREASN B:50 , LYS B:51 , LYS B:54 , ASN B:79 , SER B:161 , GLY B:194 , SER B:195 , ALA B:196 , GLY B:197 , THR B:198 , TYR B:287 , THR B:315 , GLY B:316 , GLY B:317 , HOH B:510 , HOH B:518 , HOH B:645BINDING SITE FOR RESIDUE PMP B 401
4AC4SOFTWAREASN C:50 , LYS C:51 , LYS C:54 , ASN C:79 , GLY C:194 , SER C:195 , ALA C:196 , GLY C:197 , THR C:198 , TYR C:287 , THR C:315 , GLY C:316 , GLY C:317 , HOH C:512 , HOH C:599 , HOH C:618BINDING SITE FOR RESIDUE PMP C 401
5AC5SOFTWARETYR B:30 , LEU B:31 , TYR C:30 , LEU C:31BINDING SITE FOR RESIDUE BEN C 402
6AC6SOFTWARETYR D:30 , LEU D:31 , ILE D:296BINDING SITE FOR RESIDUE BEN D 401
7AC7SOFTWAREASN D:50 , LYS D:51 , LYS D:54 , ASN D:79 , SER D:161 , GLY D:194 , SER D:195 , ALA D:196 , GLY D:197 , THR D:198 , TYR D:287 , THR D:315 , GLY D:316 , GLY D:317 , HOH D:508 , HOH D:527 , HOH D:690BINDING SITE FOR RESIDUE PMP D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D9C)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ala A:258 -Pro A:259
2His A:325 -Pro A:326
3Ala B:258 -Pro B:259
4His B:325 -Pro B:326
5Ala C:258 -Pro C:259
6His C:325 -Pro C:326
7Ala D:258 -Pro D:259
8His D:325 -Pro D:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D9C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D9C)

(-) Exons   (0, 0)

(no "Exon" information available for 4D9C)

(-) Sequences/Alignments

Asymmetric 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:328
 aligned with DCYD_SALTY | Q8ZNT7 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    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        
           DCYD_SALTY     1 MPLHHLTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
               SCOP domains d4d9ca_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...........eeehhhhhhhhh..eeeee.hhh......hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.......eeeee....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9c A   1 MPLHHLTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
                                    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        


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with DCYD_SALTY | Q8ZNT7 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:323
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325   
           DCYD_SALTY     6 LTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
               SCOP domains d4d9cb_ B: automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeehhhhhhhhh..eeeee.hhh......hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhh----...eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........eeeee....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9c B   6 LTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQC----GLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    |  185       195       205       215       225       235       245       255       265       275       285       295       305       315       325   
                                                                                                                                                                                                        180  185                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:321
 aligned with DCYD_SALTY | Q8ZNT7 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:321
                                    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 
           DCYD_SALTY     8 RFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
               SCOP domains d4d9cc_ C: automated matches                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeehhhhhhhhh..eeeee.hhh......hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........eeeee....hhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9c C   8 RFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
                                    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 


Chain D from PDB  Type:PROTEIN  Length:328
 aligned with DCYD_SALTY | Q8ZNT7 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    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        
           DCYD_SALTY     1 MPLHHLTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
               SCOP domains d4d9cd_ D: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...........eeehhhhhhhhh..eeeee.hhh......hhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh........eeeee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d9c D   1 MPLHHLTRFPRLEFIGAPTPLEYLPRLSDYLGREIYIKRDDVTPIAMGGNKLRKLEFLVADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPDAQLQTLATRIEAQGFRPYVIPVGGSSALGAMGYVESALEIAQQCEEVVGLSSVVVASGSAGTHAGLAVGLEHLMPDVELIGVTVSRSVAEQKPKVIALQQAIAGQLALTATADIHLWDDYFAPGYGVPNDAGMEAVKLLASLEGVLLDPVYTGKAMAGLIDGISQKRFNDDGPILFIHTGGAPALFAYHPHV 328
                                    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
   Legend:   → Mismatch (orange background)
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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  (1, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D9C)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DCYD_SALTY | Q8ZNT7)
molecular function
    GO:0019148    D-cysteine desulfhydrase activity    Catalysis of the reaction: D-cysteine + H2O = sulfide + NH3 + pyruvate.
    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.
    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.
biological process
    GO:0046416    D-amino acid metabolic process    The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  4d9c
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCYD_SALTY | Q8ZNT7: 4d8t 4d8u 4d8w 4d92 4d96 4d97 4d99 4d9b 4d9e 4d9f

(-) Related Entries Specified in the PDB File

4d8t SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE AT 2.2A
4d8u SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE AT 3.3 A WITH 8 PROTOMERS IN THE ASYMMETRIC UNIT
4d8w SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE SOAKED WITH D-CYS REVEALED PYRUVATE BOUND AT 4 A AWAY FROM THE ACTIVE SITE
4d92 SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE SOAKED WITH BETA-CHLORO-D-ALANINE REVEALED PYRUVATE BOUND AT 4 A AWAY FROM THE ACTIVE SITE
4d96 SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE COMPLEXED WITH AMINO CARBOXY CYCLOPROPANE (ACC)
4d97 SALMONELLA TYPHIMURIUM D-CYSTEINE DESULFHYDRASE COMPLEXED WITH D-SERINE; D-SERINE IS BOUND NON-COVALENTLY AT THE ACTIVE SITE
4d99
4d9b
4d9e
4d9f