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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE BENZOYLFORMATE DECARBOXYLASE VARIANT L461A FROM PSEUDOMONAS PUTIDA

Authors :   D. Gocke, L. Walter, K. Gauchenova, G. Kolter, M. Knoll, C. L. Berthold, G. Schneider, J. Pleiss, M. Mueller, M. Pohl

Date :   25 Jun 07 (Deposition) - 22 Jan 08 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Lyase, Calcium, Magnesium, Flavoprotein, Thiamine Pyrophosphate, Rational Protein Design, Aromatic Hydrocarbons Catabolism, Thdp-Dependent, Mandelate Pathway, Metal-Binding, Decarboxylase, Carboligation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Gocke, L. Walter, K. Gauchenova, G. Kolter, M. Knoll, C. L. Berthold G. Schneider, J. Pleiss, M. Muller, M. Pohl
Rational Protein Design Of Thdp-Dependent Enzymes- Engineering Stereoselectivity.
Chembiochem V. 9 406 2008
PubMed-ID: 18224647 | Reference-DOI: 10.1002/CBIC.200700598

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
	Atcc	:	12633
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-2/BFDL461A
	Expression System Strain	:	SG13009
	Expression System Taxid	:	562
	Expression System Variant	:	PREP4
	Expression System Vector	:	PKK233-2
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	BFD, BFDC

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	MG	6	Ligand/Ion	MAGNESIUM ION
2	SO4	4	Ligand/Ion	SULFATE ION
3	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:428 , ASN A:455 , THR A:457 , TPP A:1531 , HOH A:2226	BINDING SITE FOR RESIDUE MG A1528
02	AC2	SOFTWARE	ASN A:117 , LEU A:118 , ARG A:120 , ASN C:117 , LEU C:118 , ARG C:120	BINDING SITE FOR RESIDUE MG A1529
03	AC3	SOFTWARE	ASP B:428 , ASN B:455 , THR B:457 , TPP B:1531 , HOH B:2214	BINDING SITE FOR RESIDUE MG B1528
04	AC4	SOFTWARE	ASN B:117 , LEU B:118 , ARG B:120 , ASN D:117 , LEU D:118 , ARG D:120	BINDING SITE FOR RESIDUE MG B1529
05	AC5	SOFTWARE	ASP C:428 , ASN C:455 , THR C:457 , TPP C:1530 , HOH C:2206	BINDING SITE FOR RESIDUE MG C1528
06	AC6	SOFTWARE	ASP D:428 , ASN D:455 , THR D:457 , TPP D:1530 , HOH D:2192	BINDING SITE FOR RESIDUE MG D1528
07	AC7	SOFTWARE	HIS A:281 , PHE A:464 , TPP A:1531 , GLY C:25 , SER C:26 , HIS C:70 , LEU C:110 , HOH C:2246	BINDING SITE FOR RESIDUE SO4 C1529
08	AC8	SOFTWARE	HIS B:281 , TPP B:1531 , GLY D:25 , SER D:26 , HIS D:70 , LEU D:110	BINDING SITE FOR RESIDUE SO4 D1529
09	AC9	SOFTWARE	GLY A:25 , SER A:26 , HIS A:70 , LEU A:110 , HIS C:281 , PHE C:464 , TPP C:1530	BINDING SITE FOR RESIDUE SO4 A1530
10	BC1	SOFTWARE	GLY B:25 , SER B:26 , HIS B:70 , LEU B:110 , HOH B:2240 , HIS D:281 , TPP D:1530	BINDING SITE FOR RESIDUE SO4 B1530
11	BC2	SOFTWARE	THR A:377 , SER A:378 , GLY A:401 , LEU A:403 , GLY A:427 , ASP A:428 , GLY A:429 , SER A:430 , TYR A:433 , ASN A:455 , THR A:457 , TYR A:458 , GLY A:459 , ALA A:460 , MG A:1528 , HOH A:2190 , HOH A:2226 , ASN C:23 , PRO C:24 , GLU C:47 , HIS C:70 , ASN C:77 , SO4 C:1529	BINDING SITE FOR RESIDUE TPP A1531
12	BC3	SOFTWARE	THR B:377 , SER B:378 , GLY B:401 , LEU B:403 , GLY B:427 , ASP B:428 , GLY B:429 , SER B:430 , TYR B:433 , ASN B:455 , THR B:457 , TYR B:458 , GLY B:459 , ALA B:460 , MG B:1528 , HOH B:2176 , HOH B:2214 , ASN D:23 , PRO D:24 , GLY D:25 , GLU D:47 , HIS D:70 , ASN D:77 , SO4 D:1529	BINDING SITE FOR RESIDUE TPP B1531
13	BC4	SOFTWARE	ASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , SO4 A:1530 , THR C:377 , SER C:378 , GLY C:401 , LEU C:403 , GLY C:427 , ASP C:428 , GLY C:429 , SER C:430 , TYR C:433 , ASN C:455 , THR C:457 , TYR C:458 , GLY C:459 , ALA C:460 , MG C:1528 , HOH C:2206 , HOH C:2247	BINDING SITE FOR RESIDUE TPP C1530
14	BC5	SOFTWARE	ASN B:23 , PRO B:24 , GLU B:47 , HIS B:70 , ASN B:77 , SO4 B:1530 , THR D:377 , SER D:378 , GLY D:401 , LEU D:403 , GLY D:427 , ASP D:428 , GLY D:429 , SER D:430 , TYR D:433 , ASN D:455 , THR D:457 , TYR D:458 , GLY D:459 , ALA D:460 , MG D:1528 , HOH D:2158 , HOH D:2192	BINDING SITE FOR RESIDUE TPP D1530

(no "SS Bond" information available for 2V3W)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:120	-	Pro A:121
2	Ala A:149	-	Pro A:150
3	Val A:277	-	Phe A:278
4	Arg B:120	-	Pro B:121
5	Ala B:149	-	Pro B:150
6	Val B:277	-	Phe B:278
7	Arg C:120	-	Pro C:121
8	Ala C:149	-	Pro C:150
9	Val C:277	-	Phe C:278
10	Arg D:120	-	Pro D:121
11	Ala D:149	-	Pro D:150
12	Val D:277	-	Phe D:278

(no "SAP(SNP)/Variant" information available for 2V3W)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TPP_ENZYMES	PS00187	Thiamine pyrophosphate enzymes signature.	MDLC_PSEPU	411-430	4	A:411-430 B:411-430 C:411-430 D:411-430

(no "Exon" information available for 2V3W)

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:526
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:526
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521      
           MDLC_PSEPU     2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
               SCOP domains d2v3wa2 A:2-181 automated matches                                                                                                                                                   d2v3wa1 A:182-341 automated matches                                                                                                                             d2v3wa3 A:342-527 automated matches                                                                                                                                                        SCOP domains
               CATH domains 2v3wA01 A:2-179  [code=3.40.50.970, no name defined]                                                                                                                              2v3wA02 A:180-341 TPP-binding domain                                                                                                                              2v3wA03 A:342-527  [code=3.40.50.970, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3w A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGAARWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

Chain B from PDB  Type:PROTEIN  Length:526
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:526
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521      
           MDLC_PSEPU     2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
               SCOP domains d2v3wb2 B:2-181 automated matches                                                                                                                                                   d2v3wb1 B:182-341 automated matches                                                                                                                             d2v3wb3 B:342-527 automated matches                                                                                                                                                        SCOP domains
               CATH domains 2v3wB01 B:2-179  [code=3.40.50.970, no name defined]                                                                                                                              2v3wB02 B:180-341 TPP-binding domain                                                                                                                              2v3wB03 B:342-527  [code=3.40.50.970, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3w B   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGAARWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

Chain C from PDB  Type:PROTEIN  Length:526
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:526
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521      
           MDLC_PSEPU     2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
               SCOP domains d2v3wc2 C:2-181 automated matches                                                                                                                                                   d2v3wc1 C:182-341 automated matches                                                                                                                             d2v3wc3 C:342-527 automated matches                                                                                                                                                        SCOP domains
               CATH domains 2v3wC01 C:2-179  [code=3.40.50.970, no name defined]                                                                                                                              2v3wC02 C:180-341 TPP-binding domain                                                                                                                              2v3wC03 C:342-527  [code=3.40.50.970, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee......hhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhh...eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3w C   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGAARWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

Chain D from PDB  Type:PROTEIN  Length:526
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:526
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521      
           MDLC_PSEPU     2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
               SCOP domains d2v3wd2 D:2-181 automated matches                                                                                                                                                   d2v3wd1 D:182-341 automated matches                                                                                                                             d2v3wd3 D:342-527 automated matches                                                                                                                                                        SCOP domains
               CATH domains 2v3wD01 D:2-179  [code=3.40.50.970, no name defined]                                                                                                                              2v3wD02 D:180-341 TPP-binding domain                                                                                                                              2v3wD03 D:342-527  [code=3.40.50.970, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3w D   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGAARWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSPV 527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: DHS-like NAD/FAD-binding domain (176)

Superfamily: DHS-like NAD/FAD-binding domain (176)

Family: automated matches (36)

Protein domain: automated matches (36)

Pseudomonas putida [TaxId: 303] (1)

1a	d2v3wa1	A:182-341
1b	d2v3wb1	B:182-341
1c	d2v3wc1	C:182-341
1d	d2v3wd1	D:182-341

Fold: Thiamin diphosphate-binding fold (THDP-binding) (289)

Superfamily: Thiamin diphosphate-binding fold (THDP-binding) (289)

Family: automated matches (65)

Protein domain: automated matches (65)

Pseudomonas putida [TaxId: 303] (26)

2a	d2v3wa2	A:2-181
2b	d2v3wa3	A:342-527
2c	d2v3wb2	B:2-181
2d	d2v3wb3	B:342-527
2e	d2v3wc2	C:2-181
2f	d2v3wc3	C:342-527
2g	d2v3wd2	D:2-181
2h	d2v3wd3	D:342-527

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.970, no name defined] (144)

Pseudomonas putida. Organism_taxid: 303. (8)

1a	2v3wA03	A:342-527
1b	2v3wB03	B:342-527
1c	2v3wC03	C:342-527
1d	2v3wD03	D:342-527
1e	2v3wA01	A:2-179
1f	2v3wB01	B:2-179
1g	2v3wC01	C:2-179
1h	2v3wD01	D:2-179

Homologous Superfamily: TPP-binding domain (120)

Pseudomonas putida. Organism_taxid: 303. (8)

2a	2v3wA02	A:180-341
2b	2v3wB02	B:180-341
2c	2v3wC02	C:180-341
2d	2v3wD02	D:180-341

(no "Pfam Domain" information available for 2V3W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (MDLC_PSEPU | P20906)

molecular function
	GO:0050695	benzoylformate decarboxylase activity	Catalysis of the reaction: benzoylformate = benzaldehyde + CO2.
	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: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:0019439	aromatic compound catabolic process	The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
	GO:0019596	mandelate catabolic process	The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
	GO:0018924	mandelate metabolic process	The chemical reactions and pathways involving mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:149 - Pro A:150	[ RasMol ]
		Ala B:149 - Pro B:150	[ RasMol ]
		Ala C:149 - Pro C:150	[ RasMol ]
		Ala D:149 - Pro D:150	[ RasMol ]
		Arg A:120 - Pro A:121	[ RasMol ]
		Arg B:120 - Pro B:121	[ RasMol ]
		Arg C:120 - Pro C:121	[ RasMol ]
		Arg D:120 - Pro D:121	[ RasMol ]
		Val A:277 - Phe A:278	[ RasMol ]
		Val B:277 - Phe B:278	[ RasMol ]
		Val C:277 - Phe C:278	[ RasMol ]
		Val D:277 - Phe D:278	[ RasMol ]

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	2v3w
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1bfd	BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
1mcz	BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDACOMPLEXED WITH AN INHIBITOR, R-MANDELATE
1pi3	E28Q MUTANT BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONASPUTIDA
1po7	HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATEDECARBOXYLASE FROM PSEUDOMONAS PUTIDA
1q6z	HIGH RESOLUTION STRUCTURE OF E28A MUTANT BENZOYLFORMATEDECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITHTHIAMIN THIAZOLONE DIPHOSPHATE
1yno	HIGH RESOLUTION STRUCTURE OF BENZOYLFORMATE DECARBOXYLASEFROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMINE THIAZOLONEDIPHOSPHATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 12)

CATH Domains (2, 12)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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