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(-) Description

Title :  PHOSPHOENOLPYRUVATE CARBOXYKINASE
 
Authors :  L. W. Tari, U. Pugazenthi, H. Goldie, L. T. J. Delbaere
Date :  07 Dec 95  (Deposition) - 11 Jan 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Loop, Protein-Atp Complex, Nucleotide-Triphosphate Hydrolase, Kinase (Transphosphorylating) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. W. Tari, A. Matte, U. Pugazhenthi, H. Goldie, L. T. Delbaere
Snapshot Of An Enzyme Reaction Intermediate In The Structur Of The Atp-Mg2+-Oxalate Ternary Complex Of Escherichia Coli Pep Carboxykinase.
Nat. Struct. Biol. V. 3 355 1996
PubMed-ID: 8599762  |  Reference-DOI: 10.1038/NSB0496-355
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE
    Chains: A
    EC Number: 4.1.1.49
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: ORDERED MAGNESIUM ION OBSERVED BOUND TO ATP
    Strain: K12
    Synonym: ATP-OXALOACETATE CARBOXY-LYASE (ATP)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3OXL1Ligand/IonOXALATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:65 , TYR A:207 , LYS A:212 , LYS A:213 , ARG A:333 , HOH A:805 , HOH A:817BINDING SITE FOR RESIDUE OXL A 542
2AC2SOFTWARETHR A:255 , ATP A:544 , HOH A:702 , HOH A:822 , HOH A:875BINDING SITE FOR RESIDUE MG A 543
3AC3SOFTWARELEU A:249 , SER A:250 , GLY A:251 , THR A:252 , GLY A:253 , LYS A:254 , THR A:255 , THR A:256 , LYS A:288 , ILE A:290 , GLU A:297 , ARG A:333 , ARG A:449 , ILE A:450 , SER A:451 , ILE A:452 , THR A:455 , MG A:543 , HOH A:551 , HOH A:560 , HOH A:702 , HOH A:823 , HOH A:875BINDING SITE FOR RESIDUE ATP A 544
4ACTUNKNOWNARG A:65 , TYR A:207 , LYS A:212 , LYS A:213 , HIS A:232 , SER A:250 , LYS A:254 , THR A:255 , ASP A:268 , ASP A:269 , LYS A:288 , GLU A:297 , ARG A:333 , ARG A:449 , ILE A:450 , ILE A:452 , THR A:455PUTATIVE ACTIVE SITE RESIDUES.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:346 -Pro A:347

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_ATPPS00532 Phosphoenolpyruvate carboxykinase (ATP) signature.PCKA_ECOLI265-280  1A:265-280

(-) Exons   (0, 0)

(no "Exon" information available for 1AYL)

(-) 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:532
 aligned with PCKA_ECOLI | P22259 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:540
                                    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
           PCKA_ECOLI     1 MRVNNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL 540
               SCOP domains d1ayla2 A:1-227 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                           d1ayla1 A:228-540 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                SCOP domains
               CATH domains -----1aylA01 A:6-42,A:68-227              1aylA02              ----1aylA01 A:6-42,A:68-227 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                             1aylA03 A:228-283,A:344-538                             1aylA02 A:43-63,A:284-341                                 --1aylA03 A:228-283,A:344-538  [code=3.90.228.20, n        o name defined]                                                                                                                           -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh.....eeee...hhhhhhhh..........eee.....eee............eeee.....................eee.hhhhhhhhhhhhhhh...eeeeeeeee.......eeeeeee..hhhhhhhhhh...............eeeeee.................eeeee....eeeee.....hhhhhhhhhhhhhhhhh...eeee.eeee.....eeeee.....hhhhhh.....eeee..eeeee..eeee...eeeee.........hhhhhh.....eee.....................eeee............eeee..eeeeeee.........eee..hhhhhhhhhh.......--------.................hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhhhhh...........................hhhh........hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ayl A   1 MRVNNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLA--------PTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL 540
                                    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 |       -|      410       420       430       440       450       460       470       480       490       500       510       520       530       540
                                                                                                                                                                                                                                                                                                                                                                                                                                 392      401
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCKA_ECOLI | P22259)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCKA_ECOLI | P22259: 1aq2 1k3c 1k3d 1oen 1os1 2olq 2olr 2pxz 2py7

(-) Related Entries Specified in the PDB File

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