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(-) Description

Title :  PHOSPHOENOLPYRUVATE CARBOXYKINASE IN COMPLEX WITH ADP, ALF3 AND PYRUVATE
 
Authors :  A. M. Sudom, L. Prasad, H. Goldie, L. T. J. Delbaere
Date :  02 Oct 01  (Deposition) - 19 Dec 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase, P-Loop, Gluconeogenesis, Nucleotide-Triphosphate Hydrolase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Sudom, L. Prasad, H. Goldie, L. T. Delbaere
The Phosphoryl-Transfer Mechanism Of Escherichia Coli Phosphoenolpyruvate Carboxykinase From The Use Of Alf(3).
J. Mol. Biol. V. 314 83 2001
PubMed-ID: 11724534  |  Reference-DOI: 10.1006/JMBI.2001.5120
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE
    Chains: A
    EC Number: 4.1.1.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Strain: K12
    Expression System Taxid: 83333
    Gene: PCKA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: PEP CARBOXYKINASE, PHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2AF31Ligand/IonALUMINUM FLUORIDE
3MG1Ligand/IonMAGNESIUM ION
4PYR1Ligand/IonPYRUVIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:255 , ADP A:541 , HOH A:662 , HOH A:753 , HOH A:754 , AF3 A:999BINDING SITE FOR RESIDUE MG A 998
2AC2SOFTWARELEU 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 , GLU A:297 , THR A:441 , ARG A:449 , ILE A:450 , SER A:451 , THR A:455 , HOH A:665 , HOH A:681 , HOH A:754 , MG A:998 , AF3 A:999BINDING SITE FOR RESIDUE ADP A 541
3AC3SOFTWARELYS A:213 , HIS A:232 , SER A:250 , LYS A:254 , ASP A:269 , ARG A:333 , ADP A:541 , HOH A:662 , MG A:998BINDING SITE FOR RESIDUE AF3 A 999
4AC4SOFTWAREARG A:65 , TYR A:207 , LYS A:212 , LYS A:213 , TYR A:286 , ARG A:333 , HOH A:663 , HOH A:774BINDING SITE FOR RESIDUE PYR A 542

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K3C)

(-) 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 1K3C)

(-) 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 1K3C)

(-) 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:535
 aligned with PCKA_ECOLI | P22259 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:535
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535     
           PCKA_ECOLI     6 GLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL 540
               SCOP domains d1k3ca2 A:6-227 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                      d1k3ca1 A:228-540 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                SCOP domains
               CATH domains 1k3cA01 A:6-42,A:68-227              1k3cA02              ----1k3cA01 A:6-42,A:68-227 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                             1k3cA03 A:228-283,A:344-538                             1k3cA02 A:43-63,A:284-341                                 --1k3cA03 A:228-283,A:344-538  [code=3.90.228.20, no name defined]                                                                                                                                   -- CATH domains
               Pfam domains -------------PEPCK_ATP-1k3cA01 A:19-493                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ----------------------------------------------- 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
                 1k3c A   6 GLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL 540
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PEP-carboxyk (36)

(-) 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 1ayl 1k3d 1oen 1os1 2olq 2olr 2pxz 2py7

(-) Related Entries Specified in the PDB File

1aq2
1ayl
1k3d PHOSPHOENOLPYRUVATE CARBOXYKINASE IN COMPLEX WITH ADP AND ALF3