1YNO - JenaLib

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Title :   HIGH RESOLUTION STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA COMPLEXED WITH THIAMINE THIAZOLONE DIPHOSPHATE

Authors :   A. K. Bera, M. S. Hasson

Date :   24 Jan 05 (Deposition) - 17 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.22

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Lyase, Carbon-Carbon, Decarboxylase, Mandelate Catabolism, Thiamine Thiazolone Diphosphate, High Resolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Bera, N. L. Anderson, M. S. Hasson
High Resolution Structure Of Benzoylformate Decarboxylase From Pseudomonas Putida Complexed With Thiamine Thiazolone Diphosphate;
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKK233-2
	Expression System Strain	:	JM105
	Expression System Taxid	:	562
	Gene	:	MDLC
	Organism Scientific	:	PSEUDOMONAS PUTIDA
	Organism Taxid	:	303
	Synonym	:	BFD, BFDC

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	TZD	1	Ligand/Ion	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	TZD	4	Ligand/Ion	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:117 , LEU A:118 , ARG A:120	BINDING SITE FOR RESIDUE MG A 531
2	AC2	SOFTWARE	ASP A:428 , ASN A:455 , THR A:457 , TZD A:530 , HOH A:1002	BINDING SITE FOR RESIDUE CA A 532
3	AC3	SOFTWARE	GLU A:37 , ASP A:364 , HOH A:683 , HOH A:886 , HOH A:1059 , HOH A:1090	BINDING SITE FOR RESIDUE CA A 533
4	AC4	SOFTWARE	ASP A:347 , ALA A:416 , HOH A:623 , HOH A:724 , HOH A:816 , HOH A:841 , HOH A:861	BINDING SITE FOR RESIDUE CA A 534
5	AC5	SOFTWARE	ASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , 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 , CA A:532 , HOH A:602 , HOH A:919	BINDING SITE FOR RESIDUE TZD A 530

(no "SS Bond" information available for 1YNO)

Asymmetric Unit

No.	Residues
1	Arg A:120	-	Pro A:121
2	Ala A:149	-	Pro A:150
3	Val A:277	-	Phe A:278

(no "SAP(SNP)/Variant" information available for 1YNO)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (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

(no "Exon" information available for 1YNO)

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:524
 aligned with MDLC_PSEPU | P20906 from UniProtKB/Swiss-Prot  Length:528

    Alignment length: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    
           MDLC_PSEPU     2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 525
               SCOP domains d1ynoa2 A:2-181 automated matches                                                                                                                                                   d1ynoa1 A:182-341 Benzoylformate decarboxylase                                                                                                                  d1ynoa3 A:342-525 automated matches                                                                                                                                                      SCOP domains
               CATH domains 1ynoA01 A:2-179  [code=3.40.50.970, no name defined]                                                                                                                              1ynoA02 A:180-341 TPP-binding domain                                                                                                                              1ynoA03 A:342-525  [code=3.40.50.970, no name defined]                                                                                                                                   CATH domains
               Pfam domains -TPP_enzyme_N-1ynoA03 A:3-171                                                                                                                                             ------------------TPP_enzyme_M-1ynoA01 A:190-325                                                                                                          -------------------------------------------------TPP_enzyme_C-1ynoA02 A:375-521                                                                                                                     ---- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh..........hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.............hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TPP_ENZYMES         ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yno A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 525
                                    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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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	1ynoA03	A:342-525
1b	1ynoA01	A:2-179

Homologous Superfamily: TPP-binding domain (120)

Pseudomonas putida. Organism_taxid: 303. (8)

1ynoA02

A:180-341

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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	Cis Peptide Bonds
		Ala A:149 - Pro A:150	[ RasMol ]
		Arg A:120 - Pro A:121	[ RasMol ]
		Val A:277 - Phe A:278	[ RasMol ]

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Description

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