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(-) Description

Title :  CRYSTAL STRUCTURE OF SINGLE POINT MUTANT TYR20PHE P-COUMARIC ACID DECARBOXYLASE FROM LACTOBACILLUS PLANTARUM: STRUCTURAL INSIGHTS INTO THE ACTIVE SITE AND DECARBOXYLATION CATALYTIC MECHANISM
 
Authors :  H. Rodriguez, I. Angulo, B. De Las Rivas, N. Campillo, J. A. Paez, R. Munoz, J. M. Mancheno
Date :  27 Oct 08  (Deposition) - 17 Nov 09  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase, Active Site, Coumaric Acids, Decarboxylation, Catalytic Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rodriguez, I. Angulo, B. D Elas Rivas, N. Campillo, J. A. Paez, R. Munoz, J. M. Mancheno
P-Coumaric Acid Decarboxylase From Lactobacillus Plantarum: Structural Insights Into The Active Site And Decarboxylation Catalytic Mechanism.
Proteins V. 78 1662 2010
PubMed-ID: 20112419  |  Reference-DOI: 10.1002/PROT.22684

(-) Compounds

Molecule 1 - P-COUMARIC ACID DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 1590

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:38 , ARG B:48 , HOH B:2248BINDING SITE FOR RESIDUE ACT B 1179
2AC2SOFTWARETYR A:38 , ARG A:48 , HOH A:2248BINDING SITE FOR RESIDUE ACT A 1179
3AC3SOFTWARETYR A:18 , TYR A:26 , HOH A:2249BINDING SITE FOR RESIDUE IPA A 1180
4AC4SOFTWARETYR B:18 , TYR B:26 , HOH B:2249BINDING SITE FOR RESIDUE IPA B 1180

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W2B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:126 -Pro A:127
2Tyr B:126 -Pro B:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W2B)

(-) Exons   (0, 0)

(no "Exon" information available for 2W2B)

(-) 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:177
 aligned with F9ULL2_LACPL | F9ULL2 from UniProtKB/TrEMBL  Length:178

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
         F9ULL2_LACPL     2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRLNK 178
               SCOP domains d2w2ba_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains 2w2bA00 A:2-178  [code=2.40.128.20, no name defined]                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeeeeee..eeeeeeeeee..eeeeee......eeee.....eeeeee..eeeeeeee..eeeeeeeee...eeeeeeeee.hhhhh.hhhh...hhhhhhhhhhhhhh......eeeeeeeeeeeeee................hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2b A   2 TKTFKTLDDFLGTHFIYTFDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRLNK 178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with F9ULL2_LACPL | F9ULL2 from UniProtKB/TrEMBL  Length:178

    Alignment length:177
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       
         F9ULL2_LACPL     2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRLNK 178
               SCOP domains d2w2bb_ B: automated matches                                                                                                                                                      SCOP domains
               CATH domains 2w2bB00 B:2-178  [code=2.40.128.20, no name defined]                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.eeeeeeee..eeeeeeeeee..eeeeee......eeee.....eeeeee..eeeeeeee..eeeeeeeee...eeeeeeeee.hhhhh.hhhh...hhhhhhhhhhhhhh......eeeeeeeeeeeeee................hhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2b B   2 TKTFKTLDDFLGTHFIYTFDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRLNK 178
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W2B)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (F9ULL2_LACPL | F9ULL2)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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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    Tyr A:126 - Pro A:127   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        F9ULL2_LACPL | F9ULL2: 2gc9 2w2a 2w2f 2wsj

(-) Related Entries Specified in the PDB File

2gc9 CRYSTAL STRUCTURE OF (PC05870A) FROM LACTOBACILLUSPLANTARUM AT 1.70 A RESOLUTION
2w2a CRYSTAL STRUCTURE OF P-COUMARIC ACID DECARBOXYLASE FROM LACTOBACILLUS PLANTARUM: STRUCTURAL INSIGHTS INTO THE ACTIVE SITE AND DECARBOXYLATION CATALYTIC MECHANISM
2w2f CRYSTAL STRUCTURE OF SINGLE POINT MUTANT ARG48GLN OF P-COUMARIC ACID DECARBOXYLASE FROM LACTOBACILLUS PLANTARUM STRUCTURAL INSIGHTS INTO THE ACTIVE SITE AND DECARBOXYLATION CATALYTIC MECHANISM
2wsj CRYSTAL STRUCTURE OF SINGLE POINT MUTANT GLU71SER P-COUMARIC ACID DECARBOXYLASE FROM LACTOBACILLUS PLANTARUM: STRUCTURAL INSIGHTS INTO THE ACTIVE SITE AND DECARBOXYLATION CATALYTIC MECHANISM