2C31 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH THE COFACTOR DERIVATIVE THIAMIN-2-THIAZOLONE DIPHOSPHATE AND ADENOSINE DIPHOSPHATE

Authors :   C. L. Berthold, P. Moussatche, N. G. J. Richards, Y. Lindqvist

Date :   03 Oct 05 (Deposition) - 07 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.73

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

Keywords :   Oxalyl-Coa Decarboxylase, Oxalate, Thiamin Diphosphate, Flavoprotein, Lyase, Thiamine Pyrophosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. L. Berthold, P. Moussatche, N. G. J. Richards, Y. Lindqvist
Structural Basis For Activation Of The Thiamin Diphosphate-Dependent Enzyme Oxalyl-Coa Decarboxylase By Adenosine Diphosphate.
J. Biol. Chem. V. 280 41645 2005
PubMed-ID: 16216870 | Reference-DOI: 10.1074/JBC.M509921200
(for further references see the PDB file header)

Molecule 1 - OXALYL-COA DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET-9A
	Organism Scientific	:	OXALOBACTER FORMIGENES
	Organism Taxid	:	847
	Synonym	:	OXALYL-COENZYME A DECARBOXYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

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

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ADP	4	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
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 TRIHYDROGEN DIPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:452 , ASN A:479 , GLY A:481 , TZD A:1554 , HOH A:2353	BINDING SITE FOR RESIDUE MG A1553
2	AC2	SOFTWARE	ASP B:452 , ASN B:479 , GLY B:481 , TZD B:1554 , HOH B:2262	BINDING SITE FOR RESIDUE MG B1553
3	AC3	SOFTWARE	TYR A:377 , GLY A:400 , ALA A:401 , ASN A:402 , ALA A:403 , GLY A:426 , MET A:428 , GLY A:451 , ASP A:452 , SER A:453 , ALA A:454 , PHE A:457 , ASN A:479 , GLY A:481 , ILE A:482 , TYR A:483 , MG A:1553 , HOH A:2353 , VAL B:32 , GLU B:56 , VAL B:79 , ASN B:86 , TYR B:120 , GLU B:121	BINDING SITE FOR RESIDUE TZD A1554
4	AC4	SOFTWARE	ARG A:160 , GLY A:221 , LYS A:222 , GLY A:223 , MET A:247 , GLY A:280 , ALA A:281 , ARG A:282 , LEU A:286 , ASP A:306 , ILE A:307 , GLY A:324 , ASP A:325 , ILE A:326 , HOH A:2208 , HOH A:2354 , HOH A:2355 , HOH A:2356	BINDING SITE FOR RESIDUE ADP A1555
5	AC5	SOFTWARE	VAL A:32 , GLU A:56 , VAL A:79 , ASN A:86 , TYR A:120 , GLU A:121 , TYR B:377 , GLY B:400 , ALA B:401 , ASN B:402 , ALA B:403 , GLY B:426 , MET B:428 , GLY B:451 , ASP B:452 , SER B:453 , ALA B:454 , PHE B:457 , ASN B:479 , GLY B:481 , ILE B:482 , TYR B:483 , MG B:1553 , HOH B:2262	BINDING SITE FOR RESIDUE TZD B1554
6	AC6	SOFTWARE	ARG B:160 , GLY B:221 , LYS B:222 , GLY B:223 , MET B:247 , GLY B:280 , ALA B:281 , ARG B:282 , LEU B:286 , ASP B:306 , ILE B:307 , GLY B:324 , ASP B:325 , ILE B:326 , HOH B:2299 , HOH B:2300 , HOH B:2301 , HOH B:2302	BINDING SITE FOR RESIDUE ADP B1555

(no "SS Bond" information available for 2C31)

Asymmetric Unit

No.	Residues
1	Ile A:34	-	Pro A:35
2	Ile B:34	-	Pro B:35

(no "SAP(SNP)/Variant" information available for 2C31)

(no "PROSITE Motif" information available for 2C31)

(no "Exon" information available for 2C31)

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:546
 aligned with OXC_OXAFO | P40149 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:546
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546      
            OXC_OXAFO     7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVE 552
               SCOP domains d2c31a2 A:7-194 Oxalyl-CoA decarboxylase                                                                                                                                                    d2c31a1 A:195-369 Oxalyl-CoA decarboxylase                                                                                                                                     d2c31a3 A:370-552 Oxalyl-CoA decarboxylase                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhheeehhhhhhhh............hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhh..eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee.........................hhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c31 A   7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVE 552
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

Chain B from PDB  Type:PROTEIN  Length:547
 aligned with OXC_OXAFO | P40149 from UniProtKB/Swiss-Prot  Length:568

    Alignment length:547
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       
            OXC_OXAFO     7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
               SCOP domains d2c31b2 B:7-194 Oxalyl-CoA decarboxylase                                                                                                                                                    d2c31b1 B:195-369 Oxalyl-CoA decarboxylase                                                                                                                                     d2c31b3 B:370-553 Oxalyl-CoA decarboxylase                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhh.........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhh.eeehhhhhhhh............hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhh..eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhhhhhhh....eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee.........................hhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh..eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c31 B   7 VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHEQHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSGSSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTAVSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARAADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPDNHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQIDIQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVDGNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDNTRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFGFSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYDMMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVES 553
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

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 "CATH Domain" information available for 2C31)

(no "Pfam Domain" information available for 2C31)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OXC_OXAFO | P40149)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0008949	oxalyl-CoA decarboxylase activity	Catalysis of the reaction: H(+) + oxalyl-CoA = CO(2) + formyl-CoA.
	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:0033611	oxalate catabolic process	The chemical reactions and pathways resulting in the breakdown of oxalate, the organic acid ethanedioate.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:34 - Pro A:35	[ RasMol ]
		Ile B:34 - Pro B:35	[ RasMol ]

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	2c31
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	OXC_OXAFO \| P40149	:	2ji6 2ji7 2ji8 2ji9 2jib

(no "Related Entries Specified in the PDB File" available for 2C31)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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