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(-) Description

Title :  PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, MAD DATA
 
Authors :  P. Dunten, C. Belunis, R. Crowther, K. Hollfelder, U. Kammlott, W. Levin, H. Michel, G. B. Ramsey, A. Swain, D. Weber, S. J. Wertheimer
Date :  29 Nov 01  (Deposition) - 27 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Gluconeogenesis, P-Loop, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Dunten, C. Belunis, R. Crowther, K. Hollfelder, U. Kammlott, W. Levin, H. Michel, G. B. Ramsey, A. Swain, D. Weber, S. J. Wertheimer
Crystal Structure Of Human Cytosolic Phosphoenolpyruvate Carboxykinase Reveals A New Gtp-Binding Site.
J. Mol. Biol. V. 316 257 2002
PubMed-ID: 11851336  |  Reference-DOI: 10.1006/JMBI.2001.5364
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC (GTP)
    ChainsA
    EC Number4.1.1.32
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GenePCK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK, PEPCK-C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1GCP1Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2MN2Ligand/IonMANGANESE (II) ION
3MSE21Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:291 , GCP A:703 , HOH A:785 , HOH A:802 , HOH A:803BINDING SITE FOR RESIDUE MN A 701
2AC2SOFTWARELYS A:244 , HIS A:264 , ASP A:311 , GCP A:703 , HOH A:733 , HOH A:797BINDING SITE FOR RESIDUE MN A 702
3AC3SOFTWAREHIS A:264 , PRO A:285 , ALA A:287 , CYS A:288 , GLY A:289 , LYS A:290 , THR A:291 , ASN A:292 , ASP A:311 , VAL A:335 , ARG A:405 , ARG A:436 , TRP A:516 , PHE A:517 , PHE A:525 , GLY A:529 , PHE A:530 , ASN A:533 , MN A:701 , MN A:702 , HOH A:728 , HOH A:729 , HOH A:733 , HOH A:784 , HOH A:785 , HOH A:797 , HOH A:803 , HOH A:844BINDING SITE FOR RESIDUE GCP A 703

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021072R55QPCKGC_HUMANPolymorphism28383585AR55Q
2UniProtVAR_021073M60TPCKGC_HUMANPolymorphism28383586AM60T
3UniProtVAR_021074T138IPCKGC_HUMANPolymorphism28359542AT138I
4UniProtVAR_021075V184LPCKGC_HUMANPolymorphism707555AL184L
5UniProtVAR_015575I267VPCKGC_HUMANPolymorphism8192708AV267V
6UniProtVAR_021076E276KPCKGC_HUMANPolymorphism11552145AE276K
7UniProtVAR_021077V368IPCKGC_HUMANPolymorphism1804160AV368I
8UniProtVAR_021078P427SPCKGC_HUMANPolymorphism28359550AP427S
9UniProtVAR_042444E586DPCKGC_HUMANPolymorphism1042529AD586D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGC_HUMAN284-292  1A:284-292

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003194411aENSE00001170096chr20:56136136-56136259124PCKGC_HUMAN-00--
1.1dENST000003194411dENSE00000845753chr20:56136428-56136691264PCKGC_HUMAN1-75751A:10-7566
1.1fENST000003194411fENSE00000845754chr20:56137127-56137308182PCKGC_HUMAN75-136621A:75-13662
1.1hENST000003194411hENSE00000845755chr20:56137752-56137955204PCKGC_HUMAN136-204691A:136-20469
1.1jENST000003194411jENSE00000845756chr20:56138084-56138271188PCKGC_HUMAN204-266631A:204-26663
1.1mENST000003194411mENSE00000845757chr20:56138621-56138783163PCKGC_HUMAN267-321551A:267-32155
1.1oENST000003194411oENSE00000845758chr20:56139225-56139449225PCKGC_HUMAN321-396761A:321-39676
1.1pENST000003194411pENSE00000845759chr20:56139538-56139669132PCKGC_HUMAN396-440451A:396-44045
1.1qENST000003194411qENSE00000845760chr20:56140096-5614019196PCKGC_HUMAN440-472331A:440-46425
1.2cENST000003194412cENSE00001259794chr20:56140406-561415131108PCKGC_HUMAN472-6221511A:473-622 (gaps)150

(-) Sequences/Alignments

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:603
 aligned with PCKGC_HUMAN | P35558 from UniProtKB/Swiss-Prot  Length:622

    Alignment length:613
                                    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       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619   
          PCKGC_HUMAN    10 NLSAKVVQGSLDSLPQAVREFLENNAELCQPDHIHICDGSEEENGRLLGQMEEEGILRRLKKYDNCWLALTDPRDVARIESKTVIVTQEQRDTVPIPKTGLSQLGRWMSEEDFEKAFNARFPGCMKGRTMYVIPFSMGPLGSPLSKIGIELTDSPYVVASMRIMTRMGTPVLEAVGDGEFVKCLHSVGCPLPLQKPLVNNWPCNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRMASRLAKEEGWLAEHMLILGITNPEGEKKYLAAAFPSACGKTNLAMMNPSLPGWKVECVGDDIAWMKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAMRSEATAAAEHKGKIIMHDPFAMRPFFGYNFGKYLAHWLSMAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWMFNRIDGKASTKLTPIGYIPKEDALNLKGLGHINMMELFSISKEFWEKEVEDIEKYLEDQVNADLPCEIEREILALKQRISQM 622
               SCOP domains d1khea2 A:10-259 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                            d1khea1 A:260-622 Cytosolic phosphoenolpyruvate carboxykinase (GTP-hydrolyzing)                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1kheA01 A:10-64,A:80-259                               1kheA02        1kheA01 A:10-64,A:80-259 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                                1kheA03 A:260-329,A:415-620  [code=3.90.228.20, no name defined]      1kheA02 A:65-79,A:330-414 Phosphoenolpyruvate Carboxykinase, domain 2                1kheA03 A:260-329,A:415-620  [code=3.90.228.20, no         name defined]                                                                                                                                      -- CATH domains
               Pfam domains -------------------PEPCK-1kheA01 A:29-622                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             Pfam domains
         Sec.struct. author .hhh.eee.hhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh...ee....eeeeee..hhhhh......eeee..hhhhhh............eehhhhhhhhhhh.........eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhhhhh....eeeeee.................hhhhheeeee....eeeee...hhhhhh.......hhhhhhhhhhhh.eee..eeeeee.....eeeeeee.....hhhhhhh........eeeeee...eeeee.....eeee....eeeee........hhhhhhhh.eeeeee..eee....ee.............ee....................eeeee.hhh............eeeeeeeee.........eee..hhhhhhhhhhh.eee.--------..eee.hhhh......hhhhhhhhhhhhhhh......eeeee..............hhhhhhhhhhhhhhhhh.--.eeee..eeee.............hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------Q----T-----------------------------------------------------------------------------I---------------------------------------------L----------------------------------------------------------------------------------V--------K-------------------------------------------------------------------------------------------I----------------------------------------------------------S--------------------------------------------------------------------------------------------------------------------------------------------------------------D------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: A:10-75 UniProt: 1-75 [INCOMPLETE]                ------------------------------------------------------------Exon 1.1h  PDB: A:136-204 UniProt: 136-204                           --------------------------------------------------------------Exon 1.1m  PDB: A:267-321 UniProt: 267-321             --------------------------------------------------------------------------Exon 1.1p  PDB: A:396-440 UniProt: 396-440   -------------------------------Exon 1.2c  PDB: A:473-622 (gaps) UniProt: 472-622 [INCOMPLETE]                                                                                          Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------Exon 1.1f  PDB: A:75-136 UniProt: 75-136                      -------------------------------------------------------------------Exon 1.1j  PDB: A:204-266 UniProt: 204-266                     ------------------------------------------------------Exon 1.1o  PDB: A:321-396 UniProt: 321-396                                  -------------------------------------------Exon 1.1q  PDB: A:440-464        ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1khe A  10 NLSAKVVQGSLDSLPQAVREFLENNAELCQPDHIHICDGSEEENGRLLGQmEEEGILRRLKKYDNCWLALTDPRDVARIESKTVIVTQEQRDTVPIPKTGLSQLGRWmSEEDFEKAFNARFPGCmKGRTmYVIPFSmGPLGSPLSKIGIELTDSPYVVASmRImTRmGTPVLEALGDGEFVKCLHSVGCPLPLQKPLVNNWPCNPELTLIAHLPDRREIISFGSGYGGNSLLGKKCFALRmASRLAKEEGWLAEHmLVLGITNPEGEKKYLAAAFPSACGKTNLAmmNPSLPGWKVECVGDDIAWmKFDAQGHLRAINPENGFFGVAPGTSVKTNPNAIKTIQKNTIFTNVAETSDGGVYWEGIDEPLASGVTITSWKNKEWSSEDGEPCAHPNSRFCTPASQCPIIDAAWESPEGVPIEGIIFGGRRPAGVPLVYEALSWQHGVFVGAAmRSEA--------KIImHDPFAmRPFFGYNFGKYLAHWLSmAQHPAAKLPKIFHVNWFRKDKEGKFLWPGFGENSRVLEWmFNRIDG--STKLTPIGYIPKEDALNLKGLGHINmmELFSISKEFWDKEVEDIEKYLVDQVNADLPCEIEREILALKQRISQm 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|   |    -   |  |479  |    489       499|      509       519       529       539|     |549       559       569    || 579       589       599       609       619  |
                                                                             60-MSE                                                  117-MSE          134-MSE|      |                     170-MSE |                                                                       250-MSE        265-MSE                       295-MSE             315-MSE                                                                                                                                          460-MSE      473  |     |               500-MSE                                 540-MSE46  |                      574-MSE                                         622-MSE
                                                                                                                                                           139-MSE  |                        173-MSE                                                                                                                    296-MSE                                                                                                                                                                             476-MSE |                                                                549                       575-MSE                                           
                                                                                                                                                                  146-MSE                       176-MSE                                                                                                                                                                                                                                                                                                           482-MSE                                                                                                                                        

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCKGC_HUMAN | P35558)
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: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: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: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: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.
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCKGC_HUMAN | P355581khb 1khf 1khg 1m51 1nhx 2gmv

(-) Related Entries Specified in the PDB File

1khb PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, NATIVE DATA
1khf PEPCK COMPLEX WITH PEP
1khg PEPCK