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(-) Description

Title :  CRYSTAL STRUCTURE OF P-COUMARIC ACID DECARBOXYLASE (NP_786857.1) FROM LACTOBACILLUS PLANTARUM AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  13 Mar 06  (Deposition) - 21 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Np_786857. 1, P-Coumaric Acid Decarboxylase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of P-Coumaric Acid Decarboxylase (Np_786857. 1) From Lactobacillus Plantarum At 1. 70 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - P-COUMARIC ACID DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PC05870A
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 220668
    Strain: WCFS1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 49)

Asymmetric/Biological Unit (4, 49)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO30Ligand/Ion1,2-ETHANEDIOL
3MSE14Mod. Amino AcidSELENOMETHIONINE
4SO44Ligand/IonSULFATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:26 , TYR A:38 , ILE A:40 , VAL A:45 , ARG A:48 , GLU A:71 , THR A:75 , PHE A:94 , HOH A:224 , HOH A:317BINDING SITE FOR RESIDUE SO4 A 179
02AC2SOFTWARETYR B:26 , TYR B:38 , ILE B:40 , VAL B:45 , ARG B:48 , GLU B:71 , THR B:75 , PHE B:94 , HOH B:198 , HOH B:250BINDING SITE FOR RESIDUE SO4 B 179
03AC3SOFTWAREVAL A:130 , ALA B:55 , ASP B:56 , SER B:68 , EDO B:181 , HOH B:194 , HOH B:255BINDING SITE FOR RESIDUE SO4 B 180
04AC4SOFTWAREASP A:56 , EDO A:186 , HOH A:249 , THR B:107 , TYR B:108 , HIS B:112 , HOH B:303BINDING SITE FOR RESIDUE SO4 A 180
05AC5SOFTWAREASP A:21 , TRP A:49 , THR A:107 , TYR A:108 , HIS A:112 , GLU A:133 , PHE A:134 , ALA A:154 , HOH A:217 , HOH A:252 , HOH A:256 , VAL B:58BINDING SITE FOR RESIDUE CIT A 181
06AC6SOFTWARETHR A:4 , LYS A:6 , ASP A:10 , HOH A:274BINDING SITE FOR RESIDUE EDO A 182
07AC7SOFTWAREASN A:146 , ASN A:147 , GLU A:148 , ASP A:149 , HIS A:174 , EDO A:197 , HOH A:218 , HOH A:327BINDING SITE FOR RESIDUE EDO A 183
08AC8SOFTWARETHR A:2 , LYS A:3 , THR A:4 , PRO A:83 , ASN A:84 , LYS A:86 , MSE A:140BINDING SITE FOR RESIDUE EDO A 184
09AC9SOFTWAREMSE A:1 , THR A:2 , LYS A:86BINDING SITE FOR RESIDUE EDO A 185
10BC1SOFTWAREHIS B:34 , LYS B:54 , ALA B:55 , SO4 B:180 , HOH B:204 , HOH B:263BINDING SITE FOR RESIDUE EDO B 181
11BC2SOFTWAREASP A:56 , SO4 A:180 , HOH A:212 , HOH A:301 , VAL B:130 , EDO B:190BINDING SITE FOR RESIDUE EDO A 186
12BC3SOFTWARETYR A:108 , ASN A:136 , HOH A:319 , HOH A:323BINDING SITE FOR RESIDUE EDO A 187
13BC4SOFTWAREEDO A:189 , MSE B:59 , HOH B:206 , HOH B:277BINDING SITE FOR RESIDUE EDO A 188
14BC5SOFTWARELEU A:115 , GLN A:118 , EDO A:188 , THR B:7 , EDO B:186 , HOH B:271BINDING SITE FOR RESIDUE EDO A 189
15BC6SOFTWARELYS A:3 , ASP A:9 , ASP A:10 , LEU A:12 , THR A:14 , ASP A:142 , HOH A:222 , HOH A:239 , HOH A:330BINDING SITE FOR RESIDUE EDO A 190
16BC7SOFTWAREGLN B:53 , THR B:70 , HOH B:194 , HOH B:201 , HOH B:265BINDING SITE FOR RESIDUE EDO B 182
17BC8SOFTWAREALA A:124BINDING SITE FOR RESIDUE EDO A 191
18BC9SOFTWAREASP B:142BINDING SITE FOR RESIDUE EDO B 183
19CC1SOFTWAREASN B:136 , THR B:138BINDING SITE FOR RESIDUE EDO B 184
20CC2SOFTWAREEDO A:194 , THR B:4 , LYS B:6 , HOH B:331BINDING SITE FOR RESIDUE EDO B 185
21CC3SOFTWAREEDO A:189BINDING SITE FOR RESIDUE EDO B 186
22CC4SOFTWAREGLU A:25 , LYS A:178 , EDO A:197BINDING SITE FOR RESIDUE EDO A 192
23CC5SOFTWAREASP B:21 , LYS B:87 , ASN B:136 , HOH B:304BINDING SITE FOR RESIDUE EDO B 187
24CC6SOFTWARELYS A:6 , GLU A:62BINDING SITE FOR RESIDUE EDO A 193
25CC7SOFTWARELYS A:6 , EDO B:185BINDING SITE FOR RESIDUE EDO A 194
26CC8SOFTWAREILE B:17 , GLU B:25 , HIS B:41 , HOH B:316BINDING SITE FOR RESIDUE EDO B 188
27CC9SOFTWARETHR A:61 , HOH A:277 , HOH A:300 , HOH A:306 , GLU B:85BINDING SITE FOR RESIDUE EDO A 195
28DC1SOFTWAREASN B:84 , GLU B:85 , HOH B:302 , HOH B:320BINDING SITE FOR RESIDUE EDO B 189
29DC2SOFTWAREGLY A:23 , GLU A:148 , SER A:152 , EDO A:197 , HOH A:244BINDING SITE FOR RESIDUE EDO A 196
30DC3SOFTWAREGLU A:148 , ASP A:149 , EDO A:183 , EDO A:192 , EDO A:196 , HOH A:293 , HOH A:331BINDING SITE FOR RESIDUE EDO A 197
31DC4SOFTWARETHR A:70 , EDO A:186 , LYS B:128 , VAL B:130 , HOH B:226 , HOH B:235BINDING SITE FOR RESIDUE EDO B 190
32DC5SOFTWAREGLU A:111 , HIS A:112 , PHE A:134 , MSE B:59BINDING SITE FOR RESIDUE EDO A 198
33DC6SOFTWAREGLY B:0 , MSE B:1 , THR B:2 , LYS B:86BINDING SITE FOR RESIDUE EDO B 192
34DC7SOFTWAREGLU A:121 , ALA B:124 , THR B:125 , TYR B:126 , HOH B:309 , HOH B:328BINDING SITE FOR RESIDUE EDO B 193

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GC9)

(-) 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 2GC9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GC9)

(-) Exons   (0, 0)

(no "Exon" information available for 2GC9)

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

    Alignment length:178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        
         F9ULL2_LACPL     1 MTKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRLNK 178
               SCOP domains d2gc9a1 A:1-178 P-coumaric acid decarboxylase, pdc                                                                                                                                 SCOP domains
               CATH domains -2gc9A00 A:2-178  [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.eeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee...............hhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gc9 A   1 mTKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGmVAGRWVTDQKADIVmLTEGIYKISWTEPTGTDVALDFmPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLmEQSREKYATYPKLVVPEFANITYmGDAGQNNEDVISEAPYKEmPNDIRNGKYFDQNYHRLNK 178
                            |       10        20        30        40   |    50        60        70        80 |      90       100       110     | 120       130       140       150       160       170        
                            |                                         44-MSE         59-MSE                 82-MSE                           116-MSE                 140-MSE            159-MSE               
                            1-MSE                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with F9ULL2_LACPL | F9ULL2 from UniProtKB/TrEMBL  Length:178

    Alignment length:161
                             1                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         F9ULL2_LACPL     - -MTKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGRWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMP 160
               SCOP domains d2gc9b_ B: P-coumaric acid decarboxylase, pdc                                                                                                                     SCOP domains
               CATH domains 2gc9B00 B:0-160  [code=2.40.128.20, no name defined]                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhh.eeeeeee....eeeeeeee..eeeeeeee......eeeeee.eeeeee..eeeeeee.....eeeeeeehhh.eeeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeeeeeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gc9 B   0 GmTKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGmVAGRWVTDQKADIVmLTEGIYKISWTEPTGTDVALDFmPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLmEQSREKYATYPKLVVPEFANITYmGDAGQNNEDVISEAPYKEmP 160
                             |       9        19        29        39    |   49        59        69        79  |     89        99       109      |119       129       139|      149       159 
                             1-MSE                                     44-MSE         59-MSE                 82-MSE                           116-MSE                 140-MSE            159-MSE
   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 2GC9)

(-) 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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  Cis Peptide Bonds
    Tyr A:126 - Pro A:127   [ RasMol ]  
    Tyr B:126 - Pro B:127   [ RasMol ]  
 

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

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