2Q27 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF OXALYL-COA DECARBOXYLASE FROM ESCHERICHIA COLI

Authors :   T. Werther, A. Zimmer, G. Wille, G. Hubner, M. S. Weiss, S. Konig

Date :   26 May 07 (Deposition) - 03 Jun 08 (Release) - 18 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

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

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

Reference :   T. Werther, A. Zimmer, G. Wille, R. Golbik, M. S. Weiss, S. Konig
New Insights Into Structure-Function Relationships Of Oxaly Coa Decarboxylase From Escherichia Coli.
Febs J. V. 277 2628 2010
PubMed-ID: 20553497 | Reference-DOI: 10.1111/J.1742-464X.2010.07673.X

Molecule 1 - OXALYL-COA DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMS470-115/6/5
	Expression System Strain	:	BL21
	Expression System Vector Type	:	PLASMID
	Gene	:	YFDU
	Organism Scientific	:	ESCHERICHIA COLI
	Strain	:	K-12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 17)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	SO4	9	Ligand/Ion	SULFATE ION
5	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (4, 30)

No.	Name	Count	Type	Full Name
1	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
2	MES	4	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	18	Ligand/Ion	SULFATE ION
5	TPP	4	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:447 , ASN A:474 , GLY A:476 , HOH A:6012	BINDING SITE FOR RESIDUE MG A 1001
02	AC2	SOFTWARE	ASP B:447 , ASN B:474 , GLY B:476 , HOH B:6081	BINDING SITE FOR RESIDUE MG B 1002
03	AC3	SOFTWARE	MET A:245 , SER A:246 , ARG A:264 , ARG A:403 , HOH A:6152	BINDING SITE FOR RESIDUE SO4 A 2001
04	AC4	SOFTWARE	MET B:245 , SER B:246 , ARG B:264 , ARG B:403 , HOH B:6188	BINDING SITE FOR RESIDUE SO4 B 2002
05	AC5	SOFTWARE	ALA B:263 , PHE B:266 , HIS B:351 , ASN B:355	BINDING SITE FOR RESIDUE SO4 B 2005
06	AC6	SOFTWARE	PHE A:266 , HIS A:351 , GLN A:354 , ASN A:355	BINDING SITE FOR RESIDUE SO4 A 2006
07	AC7	SOFTWARE	ARG B:158 , LYS B:220 , GLY B:221 , GLY B:278 , ALA B:279 , ARG B:280	BINDING SITE FOR RESIDUE SO4 B 2007
08	AC8	SOFTWARE	LYS A:220 , GLY A:221 , GLY A:278 , ARG A:280 , HOH A:6204	BINDING SITE FOR RESIDUE SO4 A 2008
09	AC9	SOFTWARE	ARG A:158 , GLY A:278 , ARG A:280 , ASP A:302	BINDING SITE FOR RESIDUE SO4 A 2009
10	BC1	SOFTWARE	GLU A:54 , PRO A:80 , ASN A:84 , TYR A:372 , GLY A:395 , ALA A:396 , ASN A:397 , THR A:398 , GLY A:421 , MET A:423 , GLY A:446 , ASP A:447 , SER A:448 , ALA A:449 , PHE A:452 , ASN A:474 , GLY A:476 , ILE A:477 , TYR A:478 , HOH A:6012 , HOH A:6239	BINDING SITE FOR RESIDUE TPP A 3001
11	BC2	SOFTWARE	GLU B:54 , ASN B:84 , GLU B:119 , TYR B:372 , GLY B:395 , ALA B:396 , ASN B:397 , THR B:398 , GLY B:421 , MET B:423 , GLY B:446 , ASP B:447 , SER B:448 , ALA B:449 , PHE B:452 , ASN B:474 , GLY B:476 , ILE B:477 , TYR B:478 , HOH B:6081	BINDING SITE FOR RESIDUE TPP B 4001
12	BC3	SOFTWARE	GLY B:221 , ASP B:302 , ILE B:303 , ILE B:322 , HOH B:6139	BINDING SITE FOR RESIDUE EDO B 5001
13	BC4	SOFTWARE	GLY A:221 , TYR A:224 , SER A:225 , ILE A:303 , ILE A:322	BINDING SITE FOR RESIDUE EDO A 5002
14	BC5	SOFTWARE	ILE A:32 , PRO A:33 , THR A:35 , ASP A:36 , GLU A:549 , SER A:550 , GLY A:551	BINDING SITE FOR RESIDUE MES A 6001
15	BC6	SOFTWARE	GLY B:31 , ILE B:32 , PRO B:33 , THR B:35 , ASP B:36 , GLU B:549	BINDING SITE FOR RESIDUE MES B 6002

(no "SS Bond" information available for 2Q27)

Asymmetric Unit

No.	Residues
1	Ile A:32	-	Pro A:33
2	Gln A:368	-	Pro A:369
3	Ile B:32	-	Pro B:33
4	Gln B:368	-	Pro B:369

(no "SAP(SNP)/Variant" information available for 2Q27)

(no "PROSITE Motif" information available for 2Q27)

(no "Exon" information available for 2Q27)

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:547
 aligned with OXC_ECOLI | P0AFI0 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:547
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       
            OXC_ECOLI     5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESG 551
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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....eeeeeeehhhhhheeehhhhhhh..........eeehhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhh.......eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh.......eee.hhhh...hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...eeeeeee...........................hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q27 A   5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTESG 551
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544

Chain B from PDB  Type:PROTEIN  Length:545
 aligned with OXC_ECOLI | P0AFI0 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:545
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544     
            OXC_ECOLI     5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTE 549
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---TPP_enzyme_N-2q27B05 B:8-179                                                                                                                                                ---------------------TPP_enzyme_M-2q27B01 B:201-329                                                                                                   ----------------------------------------------------------------TPP_enzyme_C-2q27B03 B:394-540                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) ---TPP_enzyme_N-2q27B06 B:8-179                                                                                                                                                ---------------------TPP_enzyme_M-2q27B02 B:201-329                                                                                                   ----------------------------------------------------------------TPP_enzyme_C-2q27B04 B:394-540                                                                                                                     --------- Pfam domains (2)
         Sec.struct. author ..eeehhhhhhhhhhhh...eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhh........hhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhh....eeeeeeehhhhhheeehhhhhh...........eeehhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhh...eee.hhhh..........hhhhhhhhhhhh.eeeee....hhhhhhhh.......eeeeee.hhhhh.......eeee.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh.......eee........hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh..eeeeeee...........................hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh..eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q27 B   5 LQMTDGMHIIVEALKQNNIDTIYGVVGIPVTDMARHAQAEGIRYIGFRHEQSAGYAAAASGFLTQKPGICLTVSAPGFLNGLTALANATVNGFPMIMISGSSDRAIVDLQQGDYEELDQMNAAKPYAKAAFRVNQPQDLGIALARAIRVSVSGRPGGVYLDLPANVLAATMEKDEALTTIVKVENPSPALLPCPKSVTSAISLLAKAERPLIILGKGAAYSQADEQLREFIESAQIPFLPMSMAKGILEDTHPLSAAAARSFALANADVVMLVGARLNWLLAHGKKGWAADTQFIQLDIEPQEIDSNRPIAVPVVGDIASSMQGMLAELKQNTFTTPLVWRDILNIHKQQNAQKMHEKLSTDTQPLNYFNALSAVRDVLRENQDIYLVNEGANTLDNARNIIDMYKPRRRLDCGTWGVMGIGMGYAIGASVTSGSPVVAIEGDSAFGFSGMEIETICRYNLPVTIVIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDAFRGVGYNVTTTDELRHALTTGIQSRKPTIINVVIDPAAGTE 549
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2Q27)

(no "CATH Domain" information available for 2Q27)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: FAD_DHS (82)

Family: TPP_enzyme_M (50)

Escherichia coli (strain K12) (4)

1a	TPP_enzyme_M-2q27B01	B:201-329
1b	TPP_enzyme_M-2q27B02	B:201-329

Clan: THDP-binding (106)

Family: TPP_enzyme_C (54)

Escherichia coli (strain K12) (6)

2a	TPP_enzyme_C-2q27B03	B:394-540
2b	TPP_enzyme_C-2q27B04	B:394-540

Family: TPP_enzyme_N (54)

Escherichia coli (strain K12) (6)

3a	TPP_enzyme_N-2q27B05	B:8-179
3b	TPP_enzyme_N-2q27B06	B:8-179

Asymmetric Unit(hide GO term definitions)

Chain A,B (OXC_ECOLI | P0AFI0)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0071468	cellular response to acidic pH	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
	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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gln A:368 - Pro A:369	[ RasMol ]
		Gln B:368 - Pro B:369	[ RasMol ]
		Ile A:32 - Pro A:33	[ RasMol ]
		Ile B:32 - Pro B:33	[ RasMol ]

Biological Unit
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	2q27
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	OXC_ECOLI \| P0AFI0	:	2q28 2q29

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 17)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

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Pfam Domains (3, 6)

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