1YVY - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCUTRE OF ANAEROBIOSPIRILLUM SUCCINICIPRODUCENS PHOSPHOENOLPYRUVATE CARBOXYKINASE

Authors :   J. J. Cotelesage, L. Prasad, J. G. Zeikus, M. Laivenieks, L. T. Delbaere

Date :   16 Feb 05 (Deposition) - 26 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   P-Loop, Domain Movement, Kinase, Succinate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Cotelesage, L. Prasad, J. G. Zeikus, M. Laivenieks, L. T. Delbaere
Crystal Structure Of Anaerobiospirillum Succiniciproducens Pep Carboxykinase Reveals An Important Active Site Loop.
Int. J. Biochem. Cell Biol. V. 37 1829 2005
PubMed-ID: 15890557 | Reference-DOI: 10.1016/J.BIOCEL.2005.03.008
(for further references see the PDB file header)

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE [ATP]
	Chains	:	A, B
	EC Number	:	4.1.1.49
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPROEX-1
	Expression System Strain	:	DH5-ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PCKA
	Organism Scientific	:	ANAEROBIOSPIRILLUM SUCCINICIPRODUCENS
	Organism Taxid	:	13335
	Synonym	:	PEP CARBOXYKINASE, PHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YVY)

(no "Site" information available for 1YVY)

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

Asymmetric Unit

No.	Residues
1	Lys A:340	-	Pro A:341
2	Lys B:1340	-	Pro B:1341

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPCK_ATP	PS00532	Phosphoenolpyruvate carboxykinase (ATP) signature.	PCKA_ANASU	259-274	2	A:259-274 B:1259-1274

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPCK_ATP	PS00532	Phosphoenolpyruvate carboxykinase (ATP) signature.	PCKA_ANASU	259-274	1	A:259-274 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPCK_ATP	PS00532	Phosphoenolpyruvate carboxykinase (ATP) signature.	PCKA_ANASU	259-274	1	- B:1259-1274

(no "Exon" information available for 1YVY)

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:507
 aligned with PCKA_ANASU | O09460 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:517
                                    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       
          PCKA_ANASU      2 SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFFGLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGVLPPVSILSKEQTKYYFLSGFTAKLAGTERGITEPTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELKGVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF  518
               SCOP domains d1yvya1 A:2-220 automated matches                                                                                                                                                                                          d1yvya2 A:221-518 automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1yvyA01 A:2-36,A:54-220            1yvyA02          1yvyA01 A:2-36,A:54-220 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                    1yvyA03 A:221-277,A:337-518                              1yvyA02 A:37-53,A:278-336                                  1yvyA03 A:221-277,A:337-518  [code=3.90.228.20,           no name defined]                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh......eee..hhhhhhhhhh....hhhhh.ee.....eee........hhh.eeee.hhhhh.............eeehhhhhhhhhhhhhhhh....eeeeeeee.......eeeeeee.hhhhhhhhhhhh..............eeeeee....hhhhh........eeeee....eeeee....hhhhhhhhhhhhhhhhhhhh.eeee.eeee.......eeee.....hhhhhhh....eeee..eeee....eee...eeeee........hhhhhhhh....eee.....................eeeee.hhh........ee....eeeeee.........eee.hhhhhhhhhhhheee.----------..eee.hhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhh..........................hhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yvy A    2 SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFFGLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGVLPPVSILSKEQTKYYFLSGFTAK----------PTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELKGVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF  518
                                    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  |      -   |   401       411       421       431       441       451       461       471       481       491       501       511       
                                                                                                                                                                                                                                                                                                                                                                                                                        384        395

Chain B from PDB  Type:PROTEIN  Length:504
 aligned with PCKA_ANASU | O09460 from UniProtKB/Swiss-Prot  Length:532

    Alignment length:517
                                    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       
          PCKA_ANASU      2 SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFFGLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGVLPPVSILSKEQTKYYFLSGFTAKLAGTERGITEPTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELKGVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF  518
               SCOP domains d1yvyb1 B:1002-1220 automated matches                                                                                                                                                                                      d1yvyb2 B:1221-1518 automated matches                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1yvyB01 B:1002-1036,B:1054-1220    1yvyB02          1yvyB01 B:1002-1036,B:1054-1220 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                            1yvyB03 B:1221-1277,B:1337-1518                          1yvyB02 B:1037-1053,B:1278-1336                            1yvyB03 B:1221-1277,B:1337-1518  [code=3.90.228             .20, no name defined]                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eeee..hhhhhhhhhh....hhhhh.ee.....eee........hhh.eeee.hhhhh.............eeehhhhhhhhhhhhhhhh...eeeeeeeee.......eeeeeee.hhhhhhhhhhhh..............eeeeee.................eeeee....eeeee....hhhhhhhhhhhhhhhhhhh..eeee.eeee......eeeee.....hhhhhhh....eeee..eeee....eee...eeeee........hhhhhh......eee..ee.....ee..........eeeee.hhh........ee..eeeeeeee.........eee.hhhhhhhhhhhh...-------------...hhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhh..eeee....eeee..................hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yvy B 1002 SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFFGLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGVLPPVSILSKEQTKYYFLSGFTA-------------PTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELKGVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF 1518
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261      1271      1281      1291      1301      1311      1321      1331      1341      1351      1361      1371      1381 |       -     |1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511       
                                                                                                                                                                                                                                                                                                                                                                                                                      1383          1397

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 "Pfam Domain" information available for 1YVY)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PCKA_ANASU | O09460)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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: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:0004612	phosphoenolpyruvate carboxykinase (ATP) activity	Catalysis of the reaction: ATP + oxaloacetate = ADP + CO(2) + H(+) + phosphoenolpyruvate.
	GO:0004611	phosphoenolpyruvate carboxykinase activity	Catalysis of the reaction: source of phosphate + oxaloacetate = phosphoenolpyruvate + CO2 + other reaction products.
	GO:0017076	purine nucleotide binding	Interacting selectively and non-covalently with purine nucleotides, any compound consisting of a purine nucleoside esterified with (ortho)phosphate.
biological process
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1yvy)

	Sites
(no "Sites" information available for 1yvy)

	Cis Peptide Bonds
		Lys A:340 - Pro A:341	[ RasMol ]
		Lys B:1340 - Pro B:1341	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	1yvy
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	PCKA_ANASU \| O09460	:	1ytm

1ytm	STRUCTURE WITH SUBSTRATES AND COFACTORS. IN CLOSED CONFORMATION.

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