2W2F - JenaLib

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Title :   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

Authors :   H. Rodriguez, I. Angulo, B. De Las Rivas, N. Campillo, J. A. Paez, R. Mu J. M. Mancheno

Date :   29 Oct 08 (Deposition) - 09 Feb 10 (Release) - 03 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   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 Decarboxylation Catalytic Mechanism.
Proteins V. 78 1662 2010
PubMed-ID: 20112419 | Reference-DOI: 10.1002/PROT.22684

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BA	2	Ligand/Ion	BARIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	BA	-1	Ligand/Ion	BARIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	BA	-1	Ligand/Ion	BARIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:9 , ASP B:10 , LEU B:12 , HOH B:2012 , HOH B:2100 , HOH B:2101 , ASN D:172 , HOH D:2133	BINDING SITE FOR RESIDUE BA B 1177
2	AC2	SOFTWARE	ASN B:172 , ASP D:9 , ASP D:10 , LEU D:12 , HOH D:2014 , HOH D:2109 , HOH D:2110 , HOH D:2112	BINDING SITE FOR RESIDUE BA D 1177

(no "SS Bond" information available for 2W2F)

Asymmetric Unit

No.	Residues
1	Tyr A:126	-	Pro A:127
2	Tyr B:126	-	Pro B:127
3	Tyr C:126	-	Pro C:127
4	Tyr D:126	-	Pro D:127

(no "SAP(SNP)/Variant" information available for 2W2F)

(no "PROSITE Motif" information available for 2W2F)

(no "Exon" information available for 2W2F)

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: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 d2w2fa_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2w2fA00 A:2-176  [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
                 2w2f A   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGQWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 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 d2w2fb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2w2fB00 B:2-176  [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
                 2w2f B   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGQWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain C 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 d2w2fc_ C: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2w2fC00 C:2-176  [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
                 2w2f C   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGQWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 176
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain D 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 d2w2fd_ D: automated matches                                                                                                                                                    SCOP domains
               CATH domains 2w2fD00 D:2-176  [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
                 2w2f D   2 TKTFKTLDDFLGTHFIYTYDNGWEYEWYAKNDHTVDYRIHGGMVAGQWVTDQKADIVMLTEGIYKISWTEPTGTDVALDFMPNEKKLHGTIFFPKWVEEHPEITVTYQNEHIDLMEQSREKYATYPKLVVPEFANITYMGDAGQNNEDVISEAPYKEMPNDIRNGKYFDQNYHRL 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Lipocalins (514)

Superfamily: Lipocalins (514)

Family: Phenolic acid decarboxylase (PAD) (8)

Protein domain: automated matches (6)

Lactobacillus plantarum [TaxId: 1590] (3)

1a	d2w2fa_	A:
1b	d2w2fb_	B:
1c	d2w2fc_	C:
1d	d2w2fd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lipocalin (526)

Homologous Superfamily: [code=2.40.128.20, no name defined] (352)

Lactobacillus plantarum. Organism_taxid: 1590. (4)

1a	2w2fA00	A:2-176
1b	2w2fB00	B:2-176
1c	2w2fC00	C:2-176
1d	2w2fD00	D:2-176

(no "Pfam Domain" information available for 2W2F)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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.

Asymmetric Unit
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	Sites
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	Cis Peptide Bonds
		Tyr A:126 - Pro A:127	[ RasMol ]
		Tyr B:126 - Pro B:127	[ RasMol ]
		Tyr C:126 - Pro C:127	[ RasMol ]
		Tyr D:126 - Pro D:127	[ RasMol ]

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	F9ULL2_LACPL \| F9ULL2	:	2gc9 2w2a 2w2b 2wsj

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
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

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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