3FZN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   INTERMEDIATE ANALOGUE IN BENZOYLFORMATE DECARBOXYLASE

Authors :   M. Bruning, M. Berheide, D. Meyer, R. Golbik, H. Bartunik, A. Liese, K. Tittmann

Date :   26 Jan 09 (Deposition) - 05 May 09 (Release) - 05 May 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.62

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

Keywords :   Benzoylformate Decarboxylase, Thiamin Diphosphate, Intermediate Analogue, Aromatic Hydrocarbons Catabolism, Calcium, Decarboxylase, Lyase, Magnesium, Mandelate Pathway, Metal-Binding, Thiamine Pyrophosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Bruning, M. Berheide, D. Meyer, R. Golbik, H. Bartunik, A. Liese, K. Tittmann
Structural And Kinetic Studies On Native Intermediates And An Intermediate Analogue In Benzoylformate Decarboxylase Reveal A Least Motion Mechanism With An Unprecedented Short-Lived Predecarboxylation Intermediate.
Biochemistry V. 48 3258 2009
PubMed-ID: 19182954 | Reference-DOI: 10.1021/BI801957D
(for further references see the PDB file header)

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
	Chains	:	A, B, C, D
	EC Number	:	4.1.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBFD/TRC
	Expression System Strain	:	SG13009
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MDLC
	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 (5, 25)

No.	Name	Count	Type	Full Name
1	CL	11	Ligand/Ion	CHLORIDE ION
2	D7K	4	Ligand/Ion	3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(S)-HYDROXY[(R)-HYDROXY(METHOXY)PHOSPHORYL]PHENYLMETHYL}-5-(2-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:281 , 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 , LEU A:461 , PHE A:464 , HOH A:545 , MG A:605 , HOH A:1986 , ASN B:23 , PRO B:24 , GLY B:25 , SER B:26 , GLU B:47 , HIS B:70 , ASN B:77 , LEU B:110	BINDING SITE FOR RESIDUE D7K A 601
02	AC2	SOFTWARE	ASP A:428 , ASN A:455 , THR A:457 , HOH A:545 , D7K A:601	BINDING SITE FOR RESIDUE MG A 605
03	AC3	SOFTWARE	ASP A:187 , ARG D:184	BINDING SITE FOR RESIDUE CL A 704
04	AC4	SOFTWARE	ARG A:184 , ASP D:187	BINDING SITE FOR RESIDUE CL A 705
05	AC5	SOFTWARE	ASN A:117 , LEU A:118 , ARG A:120 , ASN B:117 , LEU B:118 , ARG B:120	BINDING SITE FOR RESIDUE CL A 709
06	AC6	SOFTWARE	GLN A:421 , ALA A:510 , LEU A:511 , ALA A:513 , HOH A:1992 , HOH A:2008 , HOH A:2763	BINDING SITE FOR RESIDUE CL A 710
07	AC7	SOFTWARE	GLN A:287 , LEU A:289 , LYS A:290 , PRO A:291 , HOH A:2022 , HOH A:2612 , GLN D:170 , HIS D:172 , HIS D:173	BINDING SITE FOR RESIDUE PO4 A 712
08	AC8	SOFTWARE	ASN A:23 , PRO A:24 , GLY A:25 , SER A:26 , GLU A:47 , HIS A:70 , ASN A:77 , LEU A:110 , HIS B:281 , 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 , LEU B:461 , PHE B:464 , MG B:606 , HOH B:655 , HOH B:849	BINDING SITE FOR RESIDUE D7K B 602
09	AC9	SOFTWARE	ASP B:428 , ASN B:455 , THR B:457 , D7K B:602 , HOH B:655	BINDING SITE FOR RESIDUE MG B 606
10	BC1	SOFTWARE	ASP B:187 , ARG C:184	BINDING SITE FOR RESIDUE CL B 701
11	BC2	SOFTWARE	ARG B:184 , ASP C:187	BINDING SITE FOR RESIDUE CL B 702
12	BC3	SOFTWARE	GLN B:421 , ALA B:510 , LEU B:511 , ALA B:513 , HOH B:1774 , HOH B:1990 , HOH B:2159 , HOH B:2859	BINDING SITE FOR RESIDUE CL B 703
13	BC4	SOFTWARE	ASP B:114 , ALA B:115 , ALA B:116 , HOH B:1504 , HOH B:2838	BINDING SITE FOR RESIDUE CL B 708
14	BC5	SOFTWARE	HIS C:281 , 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 , LEU C:461 , PHE C:464 , HOH C:539 , MG C:607 , HOH C:1979 , ASN D:23 , PRO D:24 , GLY D:25 , SER D:26 , GLU D:47 , HIS D:70 , ASN D:77 , LEU D:110	BINDING SITE FOR RESIDUE D7K C 604
15	BC6	SOFTWARE	ASP C:428 , ASN C:455 , THR C:457 , HOH C:539 , D7K C:604	BINDING SITE FOR RESIDUE MG C 607
16	BC7	SOFTWARE	GLN C:421 , ALA C:510 , LEU C:511 , ALA C:513 , HOH C:839 , HOH C:2021	BINDING SITE FOR RESIDUE CL C 707
17	BC8	SOFTWARE	ASN C:117 , LEU C:118 , ARG C:120 , ASN D:117 , LEU D:118 , ARG D:120	BINDING SITE FOR RESIDUE CL C 711
18	BC9	SOFTWARE	GLN B:170 , HIS B:172 , HIS B:173 , GLN C:287 , LEU C:289 , LYS C:290 , PRO C:291	BINDING SITE FOR RESIDUE PO4 C 713
19	CC1	SOFTWARE	ASP B:166 , GLN B:287 , LEU B:289 , LYS B:290 , PRO B:291 , GLN C:170 , HIS C:172 , HIS C:173 , HOH C:2139 , HOH C:2879 , HOH C:2880	BINDING SITE FOR RESIDUE PO4 C 714
20	CC2	SOFTWARE	ASP C:18 , ASP C:38 , PHE C:39 , HOH C:2929	BINDING SITE FOR RESIDUE PEG C 715
21	CC3	SOFTWARE	GLN A:335 , ALA C:218 , VAL C:221 , PRO C:243 , PRO C:392 , HOH C:710 , HOH C:859 , HOH C:1615 , HOH C:2069 , HOH C:2959 , HOH C:3178	BINDING SITE FOR RESIDUE PEG C 716
22	CC4	SOFTWARE	ASN C:23 , PRO C:24 , GLY C:25 , SER C:26 , GLU C:47 , HIS C:70 , ASN C:77 , LEU C:110 , HIS D:281 , 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 , LEU D:461 , PHE D:464 , HOH D:607 , MG D:608 , HOH D:689	BINDING SITE FOR RESIDUE D7K D 603
23	CC5	SOFTWARE	ASP D:428 , ASN D:455 , THR D:457 , D7K D:603 , HOH D:607	BINDING SITE FOR RESIDUE MG D 608
24	CC6	SOFTWARE	GLN D:421 , ALA D:510 , LEU D:511 , ALA D:513 , HOH D:733 , HOH D:2002	BINDING SITE FOR RESIDUE CL D 706
25	CC7	SOFTWARE	ASP D:18 , GLU D:37 , ASP D:38 , PHE D:39 , HOH D:2935 , HOH D:3202	BINDING SITE FOR RESIDUE PEG D 718

(no "SS Bond" information available for 3FZN)

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 3FZN)

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 3FZN)

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:523
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:523
                                    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 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
               SCOP domains d3fzna1 A:2-181 automated matches                                                                                                                                                   d3fzna2 A:182-341 Benzoylformate decarboxylase                                                                                                                  d3fzna3 A:342-524 automated matches                                                                                                                                                     SCOP domains
               CATH domains 3fznA01 A:2-179  [code=3.40.50.970, no name defined]                                                                                                                              3fznA02 A:180-341 TPP-binding domain                                                                                                                              3fznA03 A:342-524  [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.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzn A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
                                    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:523
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:523
                                    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 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
               SCOP domains d3fznb1 B:2-181 automated matches                                                                                                                                                   d3fznb2 B:182-341 Benzoylformate decarboxylase                                                                                                                  d3fznb3 B:342-524 automated matches                                                                                                                                                     SCOP domains
               CATH domains 3fznB01 B:2-179  [code=3.40.50.970, no name defined]                                                                                                                              3fznB02 B:180-341 TPP-binding domain                                                                                                                              3fznB03 B:342-524  [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.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzn B   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
                                    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:523
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:523
                                    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 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
               SCOP domains d3fznc1 C:2-181 automated matches                                                                                                                                                   d3fznc2 C:182-341 Benzoylformate decarboxylase                                                                                                                  d3fznc3 C:342-524 automated matches                                                                                                                                                     SCOP domains
               CATH domains 3fznC01 C:2-179  [code=3.40.50.970, no name defined]                                                                                                                              3fznC02 C:180-341 TPP-binding domain                                                                                                                              3fznC03 C:342-524  [code=3.40.50.970, no name defined]                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzn C   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
                                    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:523
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:523
                                    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 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
               SCOP domains d3fznd1 D:2-181 automated matches                                                                                                                                                   d3fznd2 D:182-341 Benzoylformate decarboxylase                                                                                                                  d3fznd3 D:342-524 automated matches                                                                                                                                                     SCOP domains
               CATH domains 3fznD01 D:2-179  [code=3.40.50.970, no name defined]                                                                                                                              3fznD02 D:180-341 TPP-binding domain                                                                                                                              3fznD03 D:342-524  [code=3.40.50.970, no name defined]                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhh.........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzn D   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTV 524
                                    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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Pyruvate oxidase and decarboxylase, middle domain (74)

Protein domain: Benzoylformate decarboxylase (32)

Pseudomonas putida [TaxId: 303] (32)

1a	d3fzna2	A:182-341
1b	d3fznb2	B:182-341
1c	d3fznc2	C:182-341
1d	d3fznd2	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	d3fzna1	A:2-181
2b	d3fzna3	A:342-524
2c	d3fznb1	B:2-181
2d	d3fznb3	B:342-524
2e	d3fznc1	C:2-181
2f	d3fznc3	C:342-524
2g	d3fznd1	D:2-181
2h	d3fznd3	D:342-524

Asymmetric/Biological Unit

Classes(

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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	3fznA03	A:342-524
1b	3fznA01	A:2-179
1c	3fznB01	B:2-179
1d	3fznC01	C:2-179
1e	3fznD01	D:2-179
1f	3fznB03	B:342-524
1g	3fznC03	C:342-524
1h	3fznD03	D:342-524

Homologous Superfamily: TPP-binding domain (120)

Pseudomonas putida. Organism_taxid: 303. (8)

2a	3fznA02	A:180-341
2b	3fznB02	B:180-341
2c	3fznC02	C:180-341
2d	3fznD02	D:180-341

(no "Pfam Domain" information available for 3FZN)

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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	3fzn
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	4.1.1.7
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(no "Related Entries Specified in the PDB File" available for 3FZN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 25)

Sites (25, 25)

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

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SCOP Domains (2, 12)

CATH Domains (2, 12)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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