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(-) Description

Title :  CRYSTAL STRUCTURE OF SINGLE POINT MUTANT GLU71SER P-COUMARIC ACID DECARBOXYLASE
 
Authors :  H. Rodriguez, I. Angulo, B. De Las Rivas, N. Campillo, J. A. Paez, R. Mu J. M. Mancheno
Date :  07 Sep 09  (Deposition) - 09 Feb 10  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Catalytic Mechanism, Lactic Acid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rodriguez, I. Angulo, B. De Las 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 Decarboxylatio 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
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PURI3-PDC
    Expression System Strain: JM109(DE3)(PLYSS)
    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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BA1Ligand/IonBARIUM ION
2CL1Ligand/IonCHLORIDE ION
3IPA5Ligand/IonISOPROPYL ALCOHOL
4NA4Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:21 , GLU A:103 , VAL A:106BINDING SITE FOR RESIDUE BA A 1177
02AC2SOFTWARETRP A:24 , TYR A:26 , ILE A:40 , GLY A:42 , GLY A:43 , MET A:44 , VAL A:45 , ALA A:46BINDING SITE FOR RESIDUE IPA A 1178
03AC3SOFTWARETYR A:18 , TYR A:20 , TYR A:26 , TRP A:69 , VAL A:77 , LEU A:79BINDING SITE FOR RESIDUE IPA A 1179
04AC4SOFTWARETYR A:38 , ILE A:40 , ARG A:48BINDING SITE FOR RESIDUE IPA A 1180
05AC5SOFTWAREASP A:37 , ASN A:147 , GLU A:148 , VAL A:150 , ILE A:151BINDING SITE FOR RESIDUE NA A 1181
06AC6SOFTWAREASP A:37 , ASN A:147 , GLU A:148 , VAL A:150 , ILE A:151BINDING SITE FOR RESIDUE NA A 1181
07AC7SOFTWARETYR B:18 , TYR B:20 , TYR B:26 , TRP B:69 , VAL B:77BINDING SITE FOR RESIDUE IPA B 1177
08AC8SOFTWARETYR B:38 , ARG B:48 , VAL B:77 , HOH B:2017BINDING SITE FOR RESIDUE IPA B 1178
09AC9SOFTWARETYR B:38 , GLN B:53 , SER B:71 , PRO B:72 , GLN B:109BINDING SITE FOR RESIDUE CL B 1179
10BC1SOFTWARETYR B:26 , ILE B:40 , GLY B:42 , GLY B:43 , MET B:44 , VAL B:45BINDING SITE FOR RESIDUE NA B 1180
11BC2SOFTWARETYR B:18 , THR B:19 , GLU B:25 , THR B:138 , ARG B:164BINDING SITE FOR RESIDUE NA B 1181
12BC3SOFTWARETYR A:38 , ARG A:48 , GLN A:53 , SER A:71 , PRO A:72 , GLN A:109BINDING SITE FOR RESIDUE NA A 1182

(-) SS Bonds  (0, 0)

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

(-) 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 2WSJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WSJ)

(-) 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:175
 aligned with F9ULL2_LACPL | F9ULL2 from UniProtKB/TrEMBL  Length:178

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
         F9ULL2_LACPL     2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
               SCOP domains d2wsja_ A: P-coumaric acid decarboxylase, pdc                                                                                                                                   SCOP domains
               CATH domains 2wsjA00 A:2-176  [code=2.40.128.20, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.eeeeeee....eeeeeeee..eeeeee........eeeeee.eeeeee..eeeeeee.....eeeeeeehhh.eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee...............hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsj A   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTSPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with F9ULL2_LACPL | F9ULL2 from UniProtKB/TrEMBL  Length:178

    Alignment length:175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     
         F9ULL2_LACPL     2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
               SCOP domains d2wsjb_ B: P-coumaric acid decarboxylase, pdc                                                                                                                                   SCOP domains
               CATH domains 2wsjB00 B:2-176  [code=2.40.128.20, no name defined]                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.eeeeeee....eeeeeeee..eeeeee........eeeeee.eeeeee..eeeeeee.....eeeeeeehhh.eeeeeeeehhhhhhhhhhh..hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee...............hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wsj B   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTSPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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: 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 2WSJ)

(-) 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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 Related Entries

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        F9ULL2_LACPL | F9ULL2: 2gc9 2w2a 2w2b 2w2f

(-) 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
2w2b CRYSTAL STRUCTURE OF SINGLE POINT MUTANT TYR20PHE 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