3DT2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH OXALATE AND GTP

Authors :   S. M. Sullivan, T. Holyoak

Date :   14 Jul 08 (Deposition) - 26 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Kinase, Gluconeogenesis, Lyase, Decarboxylase, Gtp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Sullivan, T. Holyoak
Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead Of Conformational Selection.
Proc. Natl. Acad. Sci. Usa V. 105 13829 2008
PubMed-ID: 18772387 | Reference-DOI: 10.1073/PNAS.0805364105

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
	Chains	:	A
	EC Number	:	4.1.1.32
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX4T2
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PCK1
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	PEPCK-C, PHOSPHOENOLPYRUVATE CARBOXYLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	GTP	1	Ligand/Ion	GUANOSINE-5'-TRIPHOSPHATE
3	MN	2	Ligand/Ion	MANGANESE (II) ION
4	NA	1	Ligand/Ion	SODIUM ION
5	OXL	1	Ligand/Ion	OXALATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:291 , HOH A:1179 , HOH A:1194 , HOH A:1242	BINDING SITE FOR RESIDUE MN A 700
2	AC2	SOFTWARE	LYS A:244 , HIS A:264 , ASP A:311	BINDING SITE FOR RESIDUE MN A 701
3	AC3	SOFTWARE	ARG A:87 , LYS A:244 , HIS A:264 , SER A:286 , ASP A:311 , ARG A:405 , ALA A:467 , HOH A:1140 , HOH A:1168 , HOH A:1198	BINDING SITE FOR RESIDUE OXL A 800
4	AC4	SOFTWARE	LEU A:79 , ASN A:208 , HOH A:1217 , HOH A:1261 , HOH A:1422	BINDING SITE FOR RESIDUE NA A 1000
5	AC5	SOFTWARE	HIS A:264 , PRO A:285 , SER A:286 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ASP A:311 , PRO A:337 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , HOH A:1114 , HOH A:1128 , HOH A:1172 , HOH A:1174 , HOH A:1179 , HOH A:1186 , HOH A:1197 , HOH A:1227 , HOH A:1242 , HOH A:1350	BINDING SITE FOR RESIDUE GTP A 900
6	AC6	SOFTWARE	LEU A:153 , TRP A:260 , TRP A:314 , MET A:315 , LYS A:316 , ARG A:324 , GLU A:424 , HOH A:1477 , HOH A:1513	BINDING SITE FOR RESIDUE 1PE A 1100

(no "SS Bond" information available for 3DT2)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:200	-	Pro A:201

(no "SAP(SNP)/Variant" information available for 3DT2)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPCK_GTP	PS00505	Phosphoenolpyruvate carboxykinase (GTP) signature.	PCKGC_RAT	284-292	1	A:284-292

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000031586	1	ENSRNOE00000330605	chr3:164012410-164012511	102	PCKGC_RAT	-	0	0	-	-
1.2	ENSRNOT00000031586	2	ENSRNOE00000271129	chr3:164012684-164012948	265	PCKGC_RAT	1-75	75	1	A:2-75	74
1.3	ENSRNOT00000031586	3	ENSRNOE00000271110	chr3:164013321-164013502	182	PCKGC_RAT	75-136	62	1	A:75-136	62
1.4	ENSRNOT00000031586	4	ENSRNOE00000271108	chr3:164014063-164014266	204	PCKGC_RAT	136-204	69	1	A:136-204	69
1.5	ENSRNOT00000031586	5	ENSRNOE00000271105	chr3:164014535-164014722	188	PCKGC_RAT	204-266	63	1	A:204-266	63
1.6	ENSRNOT00000031586	6	ENSRNOE00000271102	chr3:164015301-164015463	163	PCKGC_RAT	267-321	55	1	A:267-321	55
1.7	ENSRNOT00000031586	7	ENSRNOE00000271098	chr3:164016073-164016297	225	PCKGC_RAT	321-396	76	1	A:321-396	76
1.8	ENSRNOT00000031586	8	ENSRNOE00000271095	chr3:164016388-164016519	132	PCKGC_RAT	396-440	45	1	A:396-440	45
1.9	ENSRNOT00000031586	9	ENSRNOE00000271092	chr3:164017053-164017148	96	PCKGC_RAT	440-472	33	1	A:440-472	33
1.10	ENSRNOT00000031586	10	ENSRNOE00000271120	chr3:164017282-164018345	1064	PCKGC_RAT	472-622	151	1	A:472-622	151

Asymmetric/Biological 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:621
 aligned with PCKGC_RAT | P07379 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:621
                                    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       591       601       611       621 
            PCKGC_RAT     2 PPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
               SCOP domains d3dt2a1 A:2-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                     d3dt2a2 A:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------3dt2A01 A:11-64,A:88-259                              3dt2A02                3dt2A01 A:11-64,A:88-259 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                        3dt2A03 A:260-329,A:415-622  [code=3.90.228.20, no name defined]      3dt2A02 A:65-87,A:330-414 Phosphoenolpyruvate Carboxykinase, domain 2                3dt2A03 A:260-329,A:415-622  [code=3.90.228.20, no name defined]                                                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...eee.....eeee.........hhh.eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeeehhh.eeeee...hhhhhh..hhhhhhhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee...........eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:2-75 UniProt: 1-75 [INCOMPLETE]                          ------------------------------------------------------------Exon 1.4  PDB: A:136-204 UniProt: 136-204                            --------------------------------------------------------------Exon 1.6  PDB: A:267-321 UniProt: 267-321              --------------------------------------------------------------------------Exon 1.8  PDB: A:396-440 UniProt: 396-440    -------------------------------Exon 1.10  PDB: A:472-622 UniProt: 472-622                                                                                                              Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------Exon 1.3  PDB: A:75-136 UniProt: 75-136                       -------------------------------------------------------------------Exon 1.5  PDB: A:204-266 UniProt: 204-266                      ------------------------------------------------------Exon 1.7  PDB: A:321-396 UniProt: 321-396                                   -------------------------------------------Exon 1.9  PDB: A:440-472         ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dt2 A   2 PPQLHNGLDFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKVIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    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       591       601       611       621

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 3DT2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PCKGC_RAT | P07379)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0031406	carboxylic acid binding	Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004550	nucleoside diphosphate kinase activity	Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
	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:0004613	phosphoenolpyruvate carboxykinase (GTP) activity	Catalysis of the reaction: GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO2.
	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:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0071320	cellular response to cAMP	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 cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
	GO:0071332	cellular response to fructose stimulus	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 fructose stimulus.
	GO:0071377	cellular response to glucagon stimulus	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 glucagon stimulus.
	GO:0071456	cellular response to hypoxia	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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
	GO:0032869	cellular response to insulin stimulus	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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0071347	cellular response to interleukin-1	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 an interleukin-1 stimulus.
	GO:0051365	cellular response to potassium ion starvation	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 deprivation of potassium ions.
	GO:0071300	cellular response to retinoic acid	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 retinoic acid stimulus.
	GO:0071356	cellular response to tumor necrosis factor	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 tumor necrosis factor stimulus.
	GO:0017144	drug metabolic process	The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
	GO:0006094	gluconeogenesis	The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
	GO:0042593	glucose homeostasis	Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
	GO:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	GO:0046327	glycerol biosynthetic process from pyruvate	The chemical reactions and pathways resulting in the formation of glycerol, 1,2,3-propanetriol, from other compounds, including pyruvate.
	GO:0006475	internal protein amino acid acetylation	The addition of an acetyl group to a non-terminal amino acid in a protein.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0006165	nucleoside diphosphate phosphorylation	The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
	GO:0006107	oxaloacetate metabolic process	The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of the TCA cycle.
	GO:0061402	positive regulation of transcription from RNA polymerase II promoter in response to acidic pH	Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a pH stimulus with pH < 7.
	GO:0014823	response to activity	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
	GO:0032868	response to insulin	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0070741	response to interleukin-6	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus.
	GO:0033993	response to lipid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:1904640	response to methionine	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a methionine stimulus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Leu A:200 - Pro A:201	[ RasMol ]

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	3dt2
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3dt4	COMPLEX WITH OXALATE AND GTP, OXALATE SOAKED INTO PEPCK-GTP
3dt7	COMPLEX WITH SULFOPYRUVATE AND GTP
3dtb	COMPLEX WITH PHOSPHOGLYCOLATE AND GTP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (9, 9)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (42, 42)

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Related Entries Specified in the PDB File