2NXW - JenaLib

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Title :   CRYSTAL STRUCTURE OF PHENYLPYRUVATE DECARBOXYLASE OF AZOSPIRILLUM BRASILENSE

Authors :   W. Versees, S. Spaepen, J. Vanderleyden, J. Steyaert

Date :   20 Nov 06 (Deposition) - 29 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Thiamine Pyrophosphate, Asymmetric Dimer Of Dimers, Open Active Site Loops, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Versees, S. Spaepen, J. Vanderleyden, J. Steyaert
The Crystal Structure Of Phenylpyruvate Decarboxylase From Azospirillum Brasilense At 1. 5 A Resolution. Implications For Its Catalytic And Regulatory Mechanism.
Febs J. V. 274 2363 2007
PubMed-ID: 17403037 | Reference-DOI: 10.1111/J.1742-4658.2007.05771.X

Molecule 1 - PHENYL-3-PYRUVATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21 CODONPLUS-RP
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IPDC
	Organism Scientific	:	AZOSPIRILLUM BRASILENSE
	Organism Taxid	:	192
	Synonym	:	PHENYL-3-PYRUVATE DECARBOXYLASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:429 , ASN B:456 , SER B:458 , TPP B:2001 , HOH B:4005	BINDING SITE FOR RESIDUE MG B 4001
2	AC2	SOFTWARE	ASP A:429 , ASN A:456 , SER A:458 , TPP A:2002 , HOH A:4004	BINDING SITE FOR RESIDUE MG A 4002
3	AC3	SOFTWARE	CYS A:210 , VAL A:211 , THR A:236 , ILE A:279 , TYR A:400	BINDING SITE FOR RESIDUE CL A 4003
4	AC4	SOFTWARE	CYS B:210 , VAL B:211 , THR B:236 , ILE B:279 , TYR B:400	BINDING SITE FOR RESIDUE CL B 4004
5	AC5	SOFTWARE	PRO A:23 , GLY A:24 , GLU A:48 , ASP B:382 , ALA B:402 , MET B:404 , GLY B:428 , ASP B:429 , GLY B:430 , ALA B:431 , ASN B:456 , SER B:458 , TRP B:459 , GLU B:460 , MET B:461 , LEU B:462 , MG B:4001 , HOH B:4005 , HOH B:4026 , HOH B:4052 , HOH B:4081 , HOH B:4450	BINDING SITE FOR RESIDUE TPP B 2001
6	AC6	SOFTWARE	ASP A:382 , ALA A:402 , MET A:404 , GLY A:428 , ASP A:429 , GLY A:430 , ALA A:431 , ASN A:456 , SER A:458 , TRP A:459 , GLU A:460 , MET A:461 , LEU A:462 , MG A:4002 , HOH A:4004 , HOH A:4006 , HOH A:4014 , HOH A:4091 , HOH A:4241 , PRO B:23 , GLY B:24 , GLU B:48	BINDING SITE FOR RESIDUE TPP A 2002
7	AC7	SOFTWARE	SER B:63 , THR B:64 , PRO B:92 , ARG B:153 , SER B:156 , ARG B:215 , HOH B:4043 , HOH B:4086 , HOH B:4248	BINDING SITE FOR RESIDUE GOL B 3001
8	AC8	SOFTWARE	SER A:63 , THR A:64 , PRO A:92 , ARG A:153 , SER A:156 , HOH A:4057 , HOH A:4112	BINDING SITE FOR RESIDUE GOL A 3002
9	AC9	SOFTWARE	HIS B:43 , GLN B:415 , CYS B:416 , LEU B:445 , GLY B:446 , HOH B:4039	BINDING SITE FOR RESIDUE GOL B 3003

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

(no "Cis Peptide Bond" information available for 2NXW)

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

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

(no "Exon" information available for 2NXW)

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:537
 aligned with DCIP_AZOBR | P51852 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:546
                                   1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533      
           DCIP_AZOBR     - -------MKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDTQFQVFKEITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVNAEVEPVGDDPAWPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFDRAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQADGEPIAPMDIARAVNDRVRAGQEPLLIAADMGDCLFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFADMAAGMGGDGVRVRTRAELKAALDKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKRL 539
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee......--....-------hhhhhhhh.....eee.....hhhhhhhhhhhhhhhhh..eeeeee.hhh...............hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee.hhhh..............hhhhhhhhhhhhhhh..eeeee................hhh.eeeee..eeee..eeee..hhhhhhhhhhhh...........................hhhhhhhhhhhhhhh.....eeee..hhhhhhhh......ee.........hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhh....hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nxw A  -6 LVPRGSHMKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEG--GLLL-------DTQFQVFKEITVAQARLDDPAKAPAEIARVLGAARAQSRPVYLEIPRNMVNAEVEPVGDDPAWPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFDRAVTLGYHTYADIPLAGLVDALLERLPPSDRTTRGKEPHAYPTGLQADGEPIAPMDIARAVNDRVRAGQEPLLIAADMGDCLFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFADMAAGMGGDGVRVRTRAELKAALDKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKRL 539
                                     3        13        23        33        43        53        63        73        83        93       103 |  |  | -     | 123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533      
                                                                                                                                         105  |  |     119                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                            108  |                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                               111

Chain B from PDB  Type:PROTEIN  Length:529
 aligned with DCIP_AZOBR | P51852 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:541
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 
           DCIP_AZOBR     - ---MKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTEGNAGLLLHHQGRTLDTQFQVFKEITVAQARLDDPAKAPAEIARVLGAARALSRPVYLEIPRNMVNAEVEPVGDDPAWPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFDRAVTLGYHTYADIPLAGLVDALLEGLPPSDRTTRGKEPHAYPTGLQADGEPIAPMDIARAVNDRVRAGQEPLLIAADMGDCLFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFADMAAGMGGDGVRVRTRAELKAALDKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKR 538
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TPP_enzyme_N-2nxwB05 B:1-176                                                                                                                                                    ---------------TPP_enzyme_M-2nxwB01 B:192-328                                                                                                           --------------------------------------------------TPP_enzyme_C-2nxwB03 B:379-518                                                                                                              -------------------- Pfam domains (1)
           Pfam domains (2) ---TPP_enzyme_N-2nxwB06 B:1-176                                                                                                                                                    ---------------TPP_enzyme_M-2nxwB02 B:192-328                                                                                                           --------------------------------------------------TPP_enzyme_C-2nxwB04 B:379-518                                                                                                              -------------------- Pfam domains (2)
         Sec.struct. author ...eehhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh...eeeeeee.....----..--------hhhhhhhhh....eee.....hhhhhhhhhhhhhhhhh..eeeeee.hhh..ee...........hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhh..eee.hhhh..............hhhhhhhhhhhhhhh..eeeee...........hhhhh.....eeee..eeee..eee...hhhhhhhhhhh............................hhhhhhhhhhhhhhh.....eeee..hhhhhhhh......ee.........hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhh....hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nxw B  -2 GSHMKLAEALLRALKDRGAQAMFGIPGDFALPFFKVAEETQILPLHTLSHEPAVGFAADAAARYSSTLGVAAVTYGAGAFNMVNAVAGAYAEKSPVVVISGAPGTTE----LL--------DTQFQVFKEITVAQARLDDPAKAPAEIARVLGAARAQSRPVYLEIPRNMVNAEVEPVGDDPAWPVDRDALAACADEVLAAMRSATSPVLMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGLLADAPTPPLGTYIGVAGDAEITRLVEESDGLFLLGAILSDTNFAVSQRKIDLRKTIHAFDRAVTLGYHTYADIPLAGLVDALLERLPPSDRTTRGKEPHAYPTGLQADGEPIAPMDIARAVNDRVRAGQEPLLIAADMGDCLFTAMDMIDAGLMAPGYYAGMGFGVPAGIGAQCVSGGKRILTVVGDGAFQMTGWELGNCRRLGIDPIVILFNNASWEMLRTFQPESAFNDLDDWRFADMAAGMGGDGVRVRTRAELKAALDKAFATRGRFQLIEAMIPRGVLSDTLARFVQGQKR 538
                                     7        17        27        37        47        57        67        77        87        97      |  - ||      - |     127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537 
                                                                                                                                    104  109|      119                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                          110

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 '\|'

(no "SCOP Domain" information available for 2NXW)

(no "CATH Domain" information available for 2NXW)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: TPP_enzyme_M (50)

Azospirillum brasilense (4)

1a	TPP_enzyme_M-2nxwB01	B:192-328
1b	TPP_enzyme_M-2nxwB02	B:192-328

Clan: THDP-binding (106)

Family: TPP_enzyme_C (54)

Azospirillum brasilense (4)

2a	TPP_enzyme_C-2nxwB03	B:379-518
2b	TPP_enzyme_C-2nxwB04	B:379-518

Family: TPP_enzyme_N (54)

Azospirillum brasilense (4)

3a	TPP_enzyme_N-2nxwB05	B:1-176
3b	TPP_enzyme_N-2nxwB06	B:1-176

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCIP_AZOBR | P51852)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0047434	indolepyruvate decarboxylase activity	Catalysis of the reaction: indolepyruvate = CO2 + indole acetaldehyde.
	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.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0030976	thiamine pyrophosphate binding	Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
biological process
	GO:0009851	auxin biosynthetic process	The chemical reactions and pathways resulting in the formation of auxins, plant hormones that regulate aspects of plant growth.

Asymmetric Unit
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	Cis Peptide Bonds
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	2nxw
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	4.1.1.43
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	DCIP_AZOBR \| P51852	:	2q5j 2q5l 2q5o 2q5q 5abm

(no "Related Entries Specified in the PDB File" available for 2NXW)

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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