4GNP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH PEP AND GDP

Authors :   T. A. Johnson, T. Holyoak

Date :   17 Aug 12 (Deposition) - 03 Jul 13 (Release) - 03 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

Chains :   Asym./Biol. Unit : A

Keywords :   Kinase, Gluconeogenesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. A. Johnson, T. Holyoak
The {Omega}-Loop Lid Domain Of Phosphoenolpyruvate Carboxykinase Is Essential For Catalytic Function.
Biochemistry V. 51 9547 2012
PubMed-ID: 23127136 | Reference-DOI: 10.1021/BI301278T

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]
	Chains	:	A
	EC Number	:	4.1.1.32
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSUMO
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEE REMARK 999
	Gene	:	PCK1
	Organism Common	:	RAT
	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 (4, 5)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	NA	1	Ligand/Ion	SODIUM ION
4	PEP	1	Ligand/Ion	PHOSPHOENOLPYRUVATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:285 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , GLY A:338 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:705 , HOH A:877 , HOH A:947 , HOH A:1018 , HOH A:1029 , HOH A:1091 , HOH A:1276 , HOH A:1341 , HOH A:1359 , HOH A:1360	BINDING SITE FOR RESIDUE GDP A 701
2	AC2	SOFTWARE	LYS A:244 , HIS A:264 , ASP A:311 , HOH A:838 , HOH A:844 , HOH A:865	BINDING SITE FOR RESIDUE MN A 702
3	AC3	SOFTWARE	ALA A:86 , ARG A:87 , TYR A:235 , GLY A:236 , GLY A:237 , LYS A:244 , ASN A:403 , ARG A:405 , PHE A:485 , HOH A:838 , HOH A:844 , HOH A:871 , HOH A:930 , HOH A:1032 , HOH A:1370	BINDING SITE FOR RESIDUE PEP A 703
4	AC4	SOFTWARE	LEU A:79 , ASN A:208 , HOH A:887 , HOH A:946 , HOH A:1336	BINDING SITE FOR RESIDUE NA A 704
5	AC5	SOFTWARE	THR A:291 , ASP A:310 , GDP A:701 , HOH A:1357 , HOH A:1358 , HOH A:1359 , HOH A:1360	BINDING SITE FOR RESIDUE MN A 705

(no "SS Bond" information available for 4GNP)

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 4GNP)

(no "PROSITE Motif" information available for 4GNP)

(no "Exon" information available for 4GNP)

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
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Chain A from PDB  Type:PROTEIN  Length:605
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gnpa1 A:10-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                            d4gnpa2 A:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.......hhhhhhhhhhhh.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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gnp A  10 DFSAKVIQGSLDSLPQEVRKFVEGNAQLCQPEYIHICDGSEEEYGRLLAHMQEEGVIRKLKKYDNCWLALTDPRDVARIESKTVIITQEQRDTVPIPKSGQSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLAKIGIELTDSPYVVASMRIMTRMGTSVLEALGDGEFIKCLHSVGCPLPLKKPLVNNWACNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRIASRLAKEEGWLAEHMLILGITNPEGKKKYLAAAFPSACGKTNLAMMNPTLPGWKVECVGDDIAWMKFDAQGNLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLAPGVTITSWKNKEWRPQDEEPCAHPNSRFCTPASQCPIIDPAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEGGGIMHDPFAMRPFFGYNFGKYLAHWLSMAHRPAAKLPKIFHVNWFRKDKNGKFLWPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGLGDVNVEELFGISKEFWEKEVEEIDKYLEDQVNADLPYEIERELRALKQRISQM 622
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459      |477       487       497       507       517       527       537       547       557       567       577       587       597       607       617     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  466|                                                                                                                                                   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   475

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "CATH Domain" information available for 4GNP)

(no "Pfam Domain" information available for 4GNP)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:200 - Pro A:201	[ RasMol ]

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4gmm	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH SULFOPYRUVATE AND GTP
4gmu	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH OXALATE AND GTP
4gmw	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_1G IN COMPLEX WITH PEP AND GDP
4gmz	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH SULFOPYRUVATE AND GTP
4gnl	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH PEP AND GDP
4gnm	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_2G IN COMPLEX WITH OXALATE AND GTP
4gno	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH SULFOPYRUVATE AND GTP
4gnq	STRUCTURE OF RAT CYTOSOLIC PEPCK LD_3G IN COMPLEX WITH OXALATE AND GTP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (42, 42)

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