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(-) Description

Title :  THE STRUCTURE OF CHICKEN MITOCHONDRIAL PEPCK.
 
Authors :  T. Holyoak, S. M. Sullivan, T. Nowak
Date :  07 Dec 05  (Deposition) - 27 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Phosphoenolpyruvate Carboxykinase, Pepck, Kinase, Phosphoryl Transfer, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Holyoak, S. M. Sullivan, T. Nowak
Structural Insights Into The Mechanism Of Pepck Catalysis
Biochemistry V. 45 8254 2006
PubMed-ID: 16819824  |  Reference-DOI: 10.1021/BI060269G

(-) Compounds

Molecule 1 - PHOSPHOENOLPYRUVATE CARBOXYKINASE
    ChainsA, B
    EC Number4.1.1.32
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    Other DetailsLIVER MITOCHONDRIAL IOSZYME
    SynonymPHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK-M

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
220S1Ligand/IonBETA-D-FRUCTOFURANOSYL 6-O-OCTANOYL-ALPHA-D-GLUCOPYRANOSIDE
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
220S-1Ligand/IonBETA-D-FRUCTOFURANOSYL 6-O-OCTANOYL-ALPHA-D-GLUCOPYRANOSIDE
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MN-1Ligand/IonMANGANESE (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
220S1Ligand/IonBETA-D-FRUCTOFURANOSYL 6-O-OCTANOYL-ALPHA-D-GLUCOPYRANOSIDE
3EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:263 , HIS A:283 , CYS A:307 , ASP A:330BINDING SITE FOR RESIDUE MN A 1701
2AC2SOFTWARELYS B:263 , HIS B:283 , CYS B:307 , ASP B:330BINDING SITE FOR RESIDUE MN B 1702
3AC3SOFTWAREPHE A:467 , ARG A:470 , TRP A:576 , GLU A:630 , ARG A:637 , PHE B:467 , HIS B:471 , GLU B:630 , GLY B:633 , ARG B:637 , HOH B:1703 , HOH B:1719 , HOH B:1757 , HOH B:1824 , HOH B:1843 , HOH B:1856 , HOH B:1878 , HOH B:2034BINDING SITE FOR RESIDUE 20S B 1001
4AC4SOFTWAREARG A:323 , HIS A:325 , GLU A:541 , ARG A:543 , HOH A:2025 , HOH A:2146 , HOH A:2230 , HOH A:2236BINDING SITE FOR RESIDUE EPE A 1002
5AC5SOFTWAREALA A:104 , ARG A:105 , GLU A:107 , TYR A:254 , GLY A:256 , LYS A:262 , LYS A:263 , CYS A:307 , PHE A:352 , ASN A:422 , ARG A:424 , HOH A:1793 , HOH A:2081BINDING SITE FOR RESIDUE 1PE A 1262

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FAF)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:219 -Pro A:220
2Leu B:219 -Pro B:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FAF)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGM_CHICK303-311
 
  2A:303-311
B:303-311
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGM_CHICK303-311
 
  1A:303-311
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_GTPPS00505 Phosphoenolpyruvate carboxykinase (GTP) signature.PCKGM_CHICK303-311
 
  1-
B:303-311

(-) Exons   (0, 0)

(no "Exon" information available for 2FAF)

(-) Sequences/Alignments

Asymmetric 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:596
 aligned with PCKGM_CHICK | P21642 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:608
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633        
          PCKGM_CHICK    34 LSTSLSALPAAARDFVEEAVRLCRPREVLLCDGSEEEGKELLRGLQDDGVLHPLPKYDNCWLARTDPRDVARVESKTVLVTPEQSDAVPPPPPSGGPPQLGNWMSPNAFQAAVQERFPGCMAGRPLYVIPFSMGPPTSPLAKLGVQVTDSPYVVLSMRIMTRVGPAVLQRLDDDFVRCLHSVGRPLPLTEPLVSSWPCDRSPVLVAHIPSERRIVSFGSGYGGNSLLGKKCFALRIASRMAQQQGWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAIIFGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM 641
               SCOP domains d2fafa1 A:34-278 automated matches                                                                                                                                                                                                                   d2fafa2 A:279-641 automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2fafA01 A:34-81,A:108-277                       --2fafA02             ----2fafA01 A:34-81,A:108-277 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                     -2fafA03 A:279-349,A:435-639  [code=3.90.228.20, no name defined]       -2fafA02 A:84-103,A:351-432 Phosphoenolpyruvate Carboxykinase, domain 2            --2fafA03 A:279-349,A:435-639  [code=3.90.228.20,             no name defined]                                                                                                                                 -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eee.......eee.........hhh.eeee..hhhhh...............eehhhhhhhhhhhhh.......eeeeeeeee........eeeeeee.hhhhhhhhhhhheehhhhhh......eeeeee.................hhhhheeeeehhh.eeeee...hhhhhh.......hhhhhhhhhhhh.eee..eeeeee.....eeeeeee........hhhhh.......eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeeee........eee..hhhhhhhhhhh...------------...hhhhhhhhh..hhhhhhhhhhhhh........eeeeee.............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2faf A  34 LSTSLSALPAAARDFVEEAVRLCRPREVLLCDGSEEEGKELLRGLQDDGVLHPLPKYDNCWLARTDPRDVARVESKTVLVTPEQSDAVPPPPPSGGPPQLGNWMSPNAFQAAVQERFPGCMAGRPLYVIPFSMGPPTSPLAKLGVQVTDSPYVVLSMRIMTRVGPAVLQRLDDDFVRCLHSVGRPLPLTEPLVSSWPCDPSRVLVAHIPSERRIVSFGSGYGGNSLLGKKCFALRIASRMAQQQGWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAIIFGGRRPRGVPLVVEAFGWRHGVFMGSAMRS------------LMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM 641
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       | -         -|      503       513       523       533       543       553       563       573       583       593       603       613       623       633        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         481          494                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:596
 aligned with PCKGM_CHICK | P21642 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:608
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633        
          PCKGM_CHICK    34 LSTSLSALPAAARDFVEEAVRLCRPREVLLCDGSEEEGKELLRGLQDDGVLHPLPKYDNCWLARTDPRDVARVESKTVLVTPEQSDAVPPPPPSGGPPQLGNWMSPNAFQAAVQERFPGCMAGRPLYVIPFSMGPPTSPLAKLGVQVTDSPYVVLSMRIMTRVGPAVLQRLDDDFVRCLHSVGRPLPLTEPLVSSWPCDRSPVLVAHIPSERRIVSFGSGYGGNSLLGKKCFALRIASRMAQQQGWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAIIFGGRRPRGVPLVVEAFGWRHGVFMGSAMRSEATAAAEHKGGRLMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM 641
               SCOP domains d2fafb1 B:34-278 automated matches                                                                                                                                                                                                                   d2fafb2 B:279-641 automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2fafB01 B:34-81,B:108-277                       --2fafB02             ----2fafB01 B:34-81,B:108-277 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                                     -2fafB03 B:279-349,B:435-639  [code=3.90.228.20, no name defined]       -2fafB02 B:84-103,B:351-432 Phosphoenolpyruvate Carboxykinase, domain 2            --2fafB03 B:279-349,B:435-639  [code=3.90.228.20,             no name defined]                                                                                                                                 -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eee.......eee.........hhh.eeee..hhhhhh..............eehhhhhhhhhhhhh.......eeeeeeeee........eeeeeee.hhhhhhhhhhhh..hhhhhh......eeeeee.................hhhhheeeeehhh.eeeee...hhhhhh.......hhhhhhhhhhhh.eee..eeeeee.....eeeeeee........hhhhh.......eeeeee...eeeee.....eeee....eeeee........hhhhhhhh....eee..eee....ee.............ee.....ee.............eeeee.hhh............eeeeeeeeee........eee..hhhhhhhhhhh...------------...hhhhhhhhh..hhhhhhhhhhhhh........eeeeee.............hhhhhhhhhhhhhhhhh....eeee..eeee.............hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_GTP------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2faf B  34 LSTSLSALPAAARDFVEEAVRLCRPREVLLCDGSEEEGKELLRGLQDDGVLHPLPKYDNCWLARTDPRDVARVESKTVLVTPEQSDAVPPPPPSGGPPQLGNWMSPNAFQAAVQERFPGCMAGRPLYVIPFSMGPPTSPLAKLGVQVTDSPYVVLSMRIMTRVGPAVLQRLDDDFVRCLHSVGRPLPLTEPLVSSWPCDPSRVLVAHIPSERRIVSFGSGYGGNSLLGKKCFALRIASRMAQQQGWLAEHMLILGVTSPSGEKRYMAAAFPSACGKTNLAMMTPSLPGWRIHCVGDDIAWMKFDDEGRLRAINPERGFFGVAPGTSSRTNPNAMATIARNTIFTNVGLRSDGGVYWDGLDEPTEPGVTYTSWLGKPWKHGDPEPCAHPNSRFCAPADQCPIMDPRWDDPEGVPIDAIIFGGRRPRGVPLVVEAFGWRHGVFMGSAMRS------------LMHDPFAMRPFFGYNAGRYLEHWLSTGLRSNARLPRLFHVNWFLRDNEGRFVWPGFGHNARVLAWIFGRIQGRDTARPTPIGWVPKEGDLDLGGLPGVDYSQLFPMEKGFWEEECRQLREYYGENFGADLPRDVMAELEGLEERVRKM 641
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       | -         -|      503       513       523       533       543       553       563       573       583       593       603       613       623       633        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         481          494                                                                                                                                                   

   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, 4)

Asymmetric Unit

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FAF)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PCKGM_CHICK | P21642)
molecular function
    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: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: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:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCKGM_CHICK | P216422fah 2qzy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2FAF)