1PIX - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF THE BACTERIAL ION PUMP GLUTACONYL-COENZYME A DECARBOXYLASE

Authors :   K. S. Wendt, I. Schall, R. Huber, W. Buckel, U. Jacob

Date :   30 May 03 (Deposition) - 05 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Decarboxylase, Biotin-Dependent Ion Pump, Carboxyltransferase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. S. Wendt, I. Schall, R. Huber, W. Buckel, U. Jacob
Crystal Structure Of The Carboxyltransferase Subunit Of The Bacterial Sodium Ion Pump Glutaconyl-Coenzyme A Decarboxylase
Embo J. V. 22 3493 2003
PubMed-ID: 12853465 | Reference-DOI: 10.1093/EMBOJ/CDG358
(for further references see the PDB file header)

Molecule 1 - GLUTACONYL-COA DECARBOXYLASE A SUBUNIT
	Chains	:	A, B
	EC Number	:	4.1.1.70
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJF118HE
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GCDA
	Organism Scientific	:	ACIDAMINOCOCCUS FERMENTANS
	Organism Taxid	:	905
	Synonym	:	CARBOXYLTRANSFERASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	FMT	8	Ligand/Ion	FORMIC ACID
2	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:164 , ARG A:172 , HOH A:1009 , HOH A:1306 , ARG B:164 , ARG B:172 , HOH B:1110 , HOH B:1260 , HOH B:1305 , HOH B:1435 , HOH B:1573	BINDING SITE FOR RESIDUE SO4 B 2000
2	AC2	SOFTWARE	TYR A:268 , ALA A:269 , SER A:270 , GLY A:273	BINDING SITE FOR RESIDUE SO4 A 2001
3	AC3	SOFTWARE	GLU A:46 , ALA A:50 , ASP A:51 , LYS A:114 , HOH A:1643	BINDING SITE FOR RESIDUE SO4 A 2002
4	AC4	SOFTWARE	GLU B:46 , ALA B:50 , ASP B:51 , LYS B:114 , HOH B:1096	BINDING SITE FOR RESIDUE SO4 B 2003
5	AC5	SOFTWARE	TYR B:268 , ALA B:269 , SER B:270 , GLY B:273 , HOH B:1075	BINDING SITE FOR RESIDUE SO4 B 2004
6	AC6	SOFTWARE	THR B:137 , HIS B:443 , ILE B:444 , PRO B:445	BINDING SITE FOR RESIDUE FMT B 2005
7	AC7	SOFTWARE	THR A:137 , ILE A:444 , PRO A:445 , ASP A:469	BINDING SITE FOR RESIDUE FMT A 2006
8	AC8	SOFTWARE	ARG A:7 , TYR A:8 , HIS A:336 , ARG A:578 , HOH A:1480	BINDING SITE FOR RESIDUE FMT A 2007
9	AC9	SOFTWARE	ALA A:300 , ASN A:354 , ARG A:548 , GLU A:552	BINDING SITE FOR RESIDUE FMT A 2008

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

Asymmetric Unit

No.	Residues
1	Tyr A:371	-	Pro A:372
2	Tyr B:371	-	Pro B:372

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COA_CT_NTER	PS50980	Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.	GCDA_ACIFV	31-298	2	A:30-297 B:30-297
2	COA_CT_CTER	PS50989	Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.	GCDA_ACIFV	295-558	2	A:294-557 B:294-557

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COA_CT_NTER	PS50980	Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.	GCDA_ACIFV	31-298	2	A:30-297 B:30-297
2	COA_CT_CTER	PS50989	Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.	GCDA_ACIFV	295-558	2	A:294-557 B:294-557

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COA_CT_NTER	PS50980	Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.	GCDA_ACIFV	31-298	4	A:30-297 B:30-297
2	COA_CT_CTER	PS50989	Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.	GCDA_ACIFV	295-558	4	A:294-557 B:294-557

(no "Exon" information available for 1PIX)

Asymmetric Unit

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	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:586
 aligned with GCDA_ACIFV | Q06700 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:586
                                    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       531       541       551       561       571       581      
           GCDA_ACIFV     2 GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAWVPGQAECLLRASDTAKTLHVPLVYVLNCSGVKFDEQEKVYPNRRGGGTPFFRNAELNQLGIPVIVGIYGTNPAGGGYHSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVLEGIKKYVGMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGYVEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK 587
               SCOP domains d1pixa2 A:1-287 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                         d1pixa3 A:288-586 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1pixA01 A:1-58 Single Helix bin                           1pixA02 A:59-287 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                            1pixA03 A:288-586 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhh.....eee...............eeeeeeee..eeeeeeee.......ee..hhhhhhhhhhhhhhhhh..eeeee...ee...hhhhhh......hhhhhhhhhhhhh...eeeee..eeehhhhhhhhh..eeeee...eee................hhhhhhhhhhhhhh........hhhhhh.......eee.hhhhhhhhhhhhhhh....hhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhh.ee........eeeeeeee..eeeeeeee...ee............ee..eehhhhhhhhhhhhhhhhhh...eeeee...ee..hhhhhhhhhhhhhhhhhhhhhh....eeeee..eee.hhhhhh........eeeeee....eee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhh...ee....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------COA_CT_NTER  PDB: A:30-297 UniProt: 31-298                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COA_CT_CTER  PDB: A:294-557 UniProt: 295-558                                                                                                                                                                                                                            ----------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pix A   1 GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAWVPGQAECLLRASDTAKTLHVPLVYVLNCSGVKFDEQEKVYPNRRGGGTPFFRNAELNQLGIPVIVGIYGTNPAGGGYHSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVLEGIKKYVGMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGYVEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK 586
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

Chain B from PDB  Type:PROTEIN  Length:586
 aligned with GCDA_ACIFV | Q06700 from UniProtKB/Swiss-Prot  Length:587

    Alignment length:586
                                    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       531       541       551       561       571       581      
           GCDA_ACIFV     2 GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAWVPGQAECLLRASDTAKTLHVPLVYVLNCSGVKFDEQEKVYPNRRGGGTPFFRNAELNQLGIPVIVGIYGTNPAGGGYHSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVLEGIKKYVGMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGYVEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK 587
               SCOP domains d1pixb2 B:1-287 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                         d1pixb3 B:288-586 Glutaconyl-CoA decarboxylase A subunit                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1pixB01 B:1-58 Single Helix bin                           1pixB02 B:59-287 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                            1pixB03 B:288-586 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhhhhhh.....eee...............eeeeeeee..eeeeeeee...hhhhh...hhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhh......hhhhhhhhhhhhh...eeeee..eeehhhhhhhhh..eeeee...eee................hhhhhhhhhhhhhhhh......hhhhhh.......eee.hhhhhhhhhhhhhhhh...hhhhhh.........hhhhhhhhh........hhhhhhhhhhhhhh.ee........eeeeeeee..eeeeeeee...ee............ee..eehhhhhhhhhhhhhhhhhh...eeeee...ee..hhhhhhhhhhhhhhhhhhhhhh....eeeee..eee.hhhhhh........eeeeee....eee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhh....ee.hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------COA_CT_NTER  PDB: B:30-297 UniProt: 31-298                                                                                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------COA_CT_CTER  PDB: B:294-557 UniProt: 295-558                                                                                                                                                                                                                            ----------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pix B   1 GFYSMPRYFQNMPQVGKPLKKADAANEEQLKKIEEEIHQLIKEAQEAGKADADVNKRGELTALQRIEKLVEPGSWRPLNTLFNPQGNKNGSVAIVKGLGRVNGKWCVVVASDNKKLAGAWVPGQAECLLRASDTAKTLHVPLVYVLNCSGVKFDEQEKVYPNRRGGGTPFFRNAELNQLGIPVIVGIYGTNPAGGGYHSISPTVIIAHEKANMAVGGAGIMGGMNPKGHVDLEYANEIADMVDRTGKTEPPGAVDIHYTETGFMREVYASEEGVLEGIKKYVGMLPKYDPEFFRVDDPKAPAFPADDLYSMVPLNDKRAYDIYNVIARLFDNSELHEYKKGYGPEMVTGLAKVNGLLVGVVANVQGLLMNYPEYKAAGSVGIGGKLYRQGLVKMNEFVTLCARDRLPIVWIQDTTGIDVGNDAEKAELLGLGQSLIYSIQTSHIPQFEITLRKGTAAAHYVLGGPQGNDTNAFSIGTAATEIAVMNGETAATAMYSRRLAKDRKAGKDLQPTIDKMNNLIQAFYTKSRPKVCAELGLVDEIVDMNKIRGYVEAFTEAAYQNPESICPFHQMILPRAIREFETFVKK 586
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580

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	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(

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Superfamilies( (-)

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Organisms( (-)

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

Fold: ClpP/crotonase (207)

Superfamily: ClpP/crotonase (207)

Family: Biotin dependent carboxylase carboxyltransferase domain (32)

Protein domain: Glutaconyl-CoA decarboxylase A subunit (5)

Acidaminococcus fermentans [TaxId: 905] (1)

1a	d1pixa2	A:1-287
1b	d1pixa3	A:288-586
1c	d1pixb2	B:1-287
1d	d1pixb3	B:288-586

(no "Pfam Domain" information available for 1PIX)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GCDA_ACIFV | Q06700)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0018801	glutaconyl-CoA decarboxylase activity	Catalysis of the reaction: trans-glutaconyl-CoA + H(+) = but-2-enoyl-CoA + CO(2).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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.
biological process
	GO:0019552	glutamate catabolic process via 2-hydroxyglutarate	The anaerobic chemical reactions and pathways resulting in the breakdown of glutamate, via the intermediate 2-hydroxyglutarate, yielding energy in the form of ATP.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006814	sodium ion transport	The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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