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(-) Description

Title :  EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC
 
Authors :  M. Blaesse, T. Kupke, R. Huber, S. Steinbacher
Date :  02 Nov 00  (Deposition) - 02 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym. Unit :  A,D,G,L,M,N,O,P
Biol. Unit 1:  A,D,G,L,M,N,O,P  (3x)
Keywords :  Alpha, Beta Protein, Rossman Like Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Blaesse, T. Kupke, R. Huber, S. Steinbacher
Crystal Structure Of The Peptidyl-Cysteine Decarboxylase Epid Complexed With A Pentapeptide Substrate.
Embo J. V. 19 6299 2000
PubMed-ID: 11101502  |  Reference-DOI: 10.1093/EMBOJ/19.23.6299
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPIDERMIN MODIFYING ENZYME EPID
    Chains: A, D, G, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE12
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EPID
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS
    Organism Taxid: 1282
    Strain: TUE3298
 
Molecule 2 - LANTIBIOTIC EPIDERMIN
    Chains: M, N, O, P
    Engineered: YES
    Fragment: C-TERMINUS
    Mutation: YES
    Other Details: THE PENTAPEPTIDE WAS CHEMICALLY SYTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ADGLMNOP
Biological Unit 1 (3x): ADGLMNOP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1FMN12Ligand/IonFLAVIN MONONUCLEOTIDE
2TRS6Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:10 , ALA A:11 , SER A:12 , ILE A:13 , SER A:37 , PHE A:43 , LEU A:65 , SER A:83 , ALA A:84 , ASN A:85 , THR A:86 , CYS A:95 , ASP A:96 , THR A:101 , ASN A:115 , MET A:116 , HOH A:404 , HOH A:412 , HOH A:416 , HOH A:417 , HOH A:418 , HOH A:420 , LEU D:51 , CYS M:405BINDING SITE FOR RESIDUE FMN A 300
2AC2SOFTWARELEU A:51 , THR D:10 , ALA D:11 , SER D:12 , ILE D:13 , SER D:37 , PHE D:43 , SER D:83 , ALA D:84 , ASN D:85 , THR D:86 , ASN D:115 , MET D:116 , HOH D:304 , HOH D:306 , HOH D:308 , HOH D:312 , HOH D:313 , HOH D:329 , HOH D:332 , LEU L:64 , LEU L:65 , CYS L:95 , ASP L:96 , THR L:101 , CYS N:405BINDING SITE FOR RESIDUE FMN D 301
3AC3SOFTWARELEU D:64 , LEU D:65 , CYS D:95 , ASP D:96 , THR D:101 , HOH D:335 , THR G:10 , ALA G:11 , SER G:12 , ILE G:13 , SER G:37 , PHE G:43 , SER G:83 , ALA G:84 , ASN G:85 , THR G:86 , ASN G:115 , MET G:116 , HOH G:402 , HOH G:405 , HOH G:406 , HOH G:407 , HOH G:420 , LEU L:51 , CYS O:405BINDING SITE FOR RESIDUE FMN G 302
4AC4SOFTWARELEU G:51 , PRO G:63 , LEU G:64 , LEU G:65 , CYS G:95 , ASP G:96 , THR G:101 , THR L:10 , ALA L:11 , SER L:12 , ILE L:13 , SER L:37 , PHE L:43 , SER L:83 , ALA L:84 , ASN L:85 , THR L:86 , ASN L:115 , MET L:116 , HOH L:304 , HOH L:305 , HOH L:310 , HOH L:315 , HOH L:316 , HOH L:317 , HOH L:321 , CYS P:405BINDING SITE FOR RESIDUE FMN L 303
5AC5SOFTWARELYS D:89 , ASP D:96 , HOH D:333 , LYS G:89 , ASP G:96 , HOH G:415 , LYS L:89 , ASP L:96 , HOH L:320BINDING SITE FOR RESIDUE TRS G 401
6AC6SOFTWARELYS A:89 , ASP A:96 , HOH A:405 , HOH A:426BINDING SITE FOR RESIDUE TRS A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G5Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:80 -Pro A:81
2Leu D:80 -Pro D:81
3Leu G:80 -Pro G:81
4Leu L:80 -Pro L:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1G5Q)

(-) 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:174
 aligned with EPID_STAEP | P30197 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           EPID_STAEP     1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
               SCOP domains d1g5qa_ A: Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD                                                                                                   SCOP domains
               CATH domains 1g5qA00 A:1-174  [code=3.40.50.1950, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh.....eeeee.hhhhhh.hhhhhhhh...ee........hhhhhhhh..eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...ee...eeeeeee....eeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1g5q A   1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNNINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain D from PDB  Type:PROTEIN  Length:174
 aligned with EPID_STAEP | P30197 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           EPID_STAEP     1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
               SCOP domains d1g5qd_ D: Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD                                                                                                   SCOP domains
               CATH domains 1g5qD00 D:1-174  [code=3.40.50.1950, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh.....eeeee.hhhhhh.hhhhhhhh...ee........hhhhhhhh..eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...ee...eeeeeee.....eeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1g5q D   1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNNINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain G from PDB  Type:PROTEIN  Length:174
 aligned with EPID_STAEP | P30197 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           EPID_STAEP     1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
               SCOP domains d1g5qg_ G: Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD                                                                                                   SCOP domains
               CATH domains 1g5qG00 G:1-174  [code=3.40.50.1950, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh.....eeeee.hhhhhh.hhhhhhhh...ee........hhhhhhhh..eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...ee...eeeeeee.....eeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1g5q G   1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNNINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain L from PDB  Type:PROTEIN  Length:174
 aligned with EPID_STAEP | P30197 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
           EPID_STAEP     1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNHINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
               SCOP domains d1g5ql_ L: Epidermin modifying enzyme (peptidyl-cysteine decarboxylase) EpiD                                                                                                   SCOP domains
               CATH domains 1g5qL00 L:1-174  [code=3.40.50.1950, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh.....eeeee.hhhhhh.hhhhhhhh...ee........hhhhhhhh..eeeeeeehhhhhhhhhh....hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhh...ee...eeeeeee....eeeeeee..hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1g5q L   1 MYGKLLICATASINVININHYIVELKQHFDEVNILFSPSSKNFINTDVLKLFCDNLYDEIKDPLLNNINIVENHEYILVLPASANTINKIANGICDNLLTTVCLTGYQKLFIFPNMNIRMWGNPFLQKNIDLLKNNDVKVYSPDMNKSFEISSGRYKNNITMPNIENVLNFVLN 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    


Chain M from PDB  Type:PROTEIN  Length:5
 aligned with LANE_STAEP | P08136 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:5
           LANE_STAEP    48 NSYCC  52
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1g5q M 401 DSYTC 405


Chain N from PDB  Type:PROTEIN  Length:5
 aligned with LANE_STAEP | P08136 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:5
           LANE_STAEP    48 NSYCC  52
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1g5q N 401 DSYTC 405


Chain O from PDB  Type:PROTEIN  Length:5
 aligned with LANE_STAEP | P08136 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:5
           LANE_STAEP    48 NSYCC  52
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1g5q O 401 DSYTC 405


Chain P from PDB  Type:PROTEIN  Length:5
 aligned with LANE_STAEP | P08136 from UniProtKB/Swiss-Prot  Length:52

    Alignment length:5
           LANE_STAEP    48 NSYCC  52
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..ee. Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1g5q P 401 DSYTC 405
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G5Q)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,D,G,L   (EPID_STAEP | P30197)
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.

Chain M,N,O,P   (LANE_STAEP | P08136)
molecular function
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1g5q
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 Related Entries

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

UniProtKB/Swiss-Prot
        EPID_STAEP | P30197: 1g63

(-) Related Entries Specified in the PDB File

1g63 PEPTIDYL-CYSTEINE DECARBOXYLASE EPID