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(-) Description

Title :  CRYSTAL STRUCTURE OF ATP-DEPENDENT PHOSPHOENOLPYRUVATE CARBOXYKINASE FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Sugahara, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Sep 04  (Deposition) - 11 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphoenolpyruvate Carboxykinase, Adenosine Triphosphate, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sugahara, N. Ohshima, Y. Ukita, M. Sugahara, N. Kunishima
Structure Of Atp-Dependent Phosphoenolpyruvate Carboxykinas From Thermus Thermophilus Hb8 Showing The Structural Basis Of Induced Fit And Thermostability.
Acta Crystallogr. , Sect. D V. 61 1500 2005
PubMed-ID: 16239727  |  Reference-DOI: 10.1107/S090744490502651X

(-) Compounds

Molecule 1 - ATP-DEPENDENT PHOSPHOENOLPYRUVATE CARBOXYKINASE
    Chains: A, B
    EC Number: 4.1.1.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA2Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
4PO46Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:130 , ASN A:131 , PHE A:133 , GLY A:267 , HOH A:3067 , HOH A:3311BINDING SITE FOR RESIDUE CA A 2001
02AC2SOFTWAREARG B:130 , ASN B:131 , PHE B:133 , GLY B:267 , HOH B:4040 , HOH B:4144BINDING SITE FOR RESIDUE CA B 2002
03AC3SOFTWAREVAL A:20 , SER A:21 , ARG A:130 , ARG A:137 , HOH A:3008 , HOH A:3015 , HOH A:3046 , HOH A:3220 , HIS B:38BINDING SITE FOR RESIDUE PO4 A 3001
04AC4SOFTWAREGLU A:259 , LYS A:413 , LYS A:416 , HIS A:417 , HOH A:3108BINDING SITE FOR RESIDUE PO4 A 3002
05AC5SOFTWAREHIS A:38 , HOH A:3037 , HOH A:3047 , HOH A:3221 , SER B:21 , PRO B:22 , ARG B:130 , ARG B:137BINDING SITE FOR RESIDUE PO4 B 3003
06AC6SOFTWARELYS B:413 , LYS B:416 , HIS B:417 , HOH B:4353BINDING SITE FOR RESIDUE PO4 B 3004
07AC7SOFTWARELEU B:233 , SER B:234 , GLY B:235 , THR B:236 , GLY B:237 , LYS B:238 , THR B:239 , HOH B:4163 , HOH B:4193 , HOH B:4227 , HOH B:4236 , HOH B:4347BINDING SITE FOR RESIDUE PO4 B 3005
08AC8SOFTWAREGLU B:5 , HIS B:10 , LYS B:12BINDING SITE FOR RESIDUE PO4 B 3006
09AC9SOFTWARELEU A:233 , SER A:234 , GLY A:235 , THR A:236 , GLY A:237 , LYS A:238 , THR A:239 , THR A:240 , LYS A:272 , THR A:426 , ARG A:438 , PHE A:439 , THR A:444 , HOH A:3339BINDING SITE FOR RESIDUE ATP A 1001
10BC1SOFTWAREPHE B:160 , GLN B:161 , ARG B:166 , HOH B:4130 , HOH B:4166 , HOH B:4258BINDING SITE FOR RESIDUE GOL B 4001
11BC2SOFTWAREGLU A:66 , GLY A:67 , TRP A:71 , HOH A:3044 , THR B:50 , GLY B:51 , THR B:315 , HOH B:4058 , HOH B:4064BINDING SITE FOR RESIDUE GOL B 4002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:47 -Pro A:48
2Thr B:47 -Pro B:48

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPCK_ATPPS00532 Phosphoenolpyruvate carboxykinase (ATP) signature.PCKA_THET8249-264
 		  2A:249-264
B:249-264

(-) Exons   (0, 0)

(no "Exon" information available for 1XKV)

(-) 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:515
 aligned with PCKA_THET8 | Q5SLL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:528
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521        
           PCKA_THET8     2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARVAGTERGVTEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRTE 529
               SCOP domains d1xkva2 A:2-211 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                          d1xkva1 A:212-529 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1xkvA01 A:2-33,A:55-211         1xkvA02          ----1xkvA01 A:2-33,A:55-211 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                          1xkvA03 A:212-267,A:330-526                             1xkvA02 A:34-50,A:268-327                                   --1xkvA03 A:212-267,A:330-526  [code=3.90.228.20,        no name defined]                                                                                                                              --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh......eee..hhhhhhhhhhhh...ee.....eee........hhh.eeee...............eeehhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeeeee.hhhhhhhhhhhh.hhhhhh------.....eeeeee.....hhhhhh.....eeeee....eeeee....hhhhhhhhhhhhhhhhhhh..eeee.eeee.....eeeeee....hhhhhh......eee..eeee....eee...eeeee........hhhhhhhhh....eee..ee......ee..........eeeee.hhh.......ee..eeeeeeee.........eeeehhhhhhhhhhhheeee.-------...eeee.hhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..ee.......ee.hhhhhhhhhhhhhhhhhhhh.eee......eee......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xkv A   2 QRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFG------AFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARV-------TEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRTE 529
                                    11        21        31        41        51        61        71        81        91       101       111       121       131        |-     | 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371    |    -  |    391       401       411       421       431       441       451       461       471       481       491       501       511       521        
                                                                                                                                                                    140    147                                                                                                                                                                                                                                  376     384                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:519
 aligned with PCKA_THET8 | Q5SLL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:528
                                    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        
           PCKA_THET8     1 MQRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARVAGTERGVTEPRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT 528
               SCOP domains d1xkvb2 B:1-211 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                           d1xkvb1 B:212-528 Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1xkvB01 B:1-33,B:55-211          1xkvB02          ----1xkvB01 B:1-33,B:55-211 Phosphoenolpyruvate Carboxykinase, domain 1                                                                                          1xkvB03 B:212-267,B:330-526                             1xkvB02 B:34-50,B:268-327                                   --1xkvB03 B:212-267,B:330-526  [code=3.90.228.20,          no name defined]                                                                                                                            -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh......eee..hhhhhhhhhhhh...ee.....eee........hhh.eeee...............eeehhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeeeee.hhhhhhhhhhhh.hhhhh............eeeeee.....hhhhhh.....eeeee....eeeee....hhhhhhhhhhhhhhhhhhh..eeee.eeee.....eeeee.....hhhhhhh.....eee..eeee....eee...eeeee........hhhhhhhhh....eee..ee......ee..........eeeee.hhh.......ee..eeeeeeee.........eee.hhhhhhhhhhhheeee.---------.eeee.hhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeee..ee.......ee.hhhhhhhhhhhhhhhhhhh..eee......eee......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PEPCK_ATP       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1xkv B   1 MQRLEALGIHPKKRVFWNTVSPVLVEHTLLRGEGLLAHHGPLVVDTTPYTGRSPKDKFVVREPEVEGEIWWGEVNQPFAPEAFEALYQRVVQYLSERDLYVQDLYAGADRRYRLAVRVVTESPWHALFARNMFILPRRFGNDDEVEAFVPGFTVVHAPYFQAVPERDGTRSEVFVGISFQRRLVLIVGTKYAGEIKKSIFTVMNYLMPKRGVFPMHASANVGKEGDVAVFFGLSGTGKTTLSTDPERPLIGDDEHGWSEDGVFNFEGGCYAKVIRLSPEHEPLIYKASNQFEAILENVVVNPESRRVQWDDDSKTENTRSSYPIAHLENVVESGVAGHPRAIFFLSADAYGVLPPIARLSPEEAMYYFLSGYTARV---------PRATFSACFGAPFLPMHPGVYARMLGEKIRKHAPRVYLVNTGWTGGPYGVGYRFPLPVTRALLKAALSGALENVPYRRDPVFGFEVPLEAPGVPQELLNPRETWADKEAYDQQARKLARLFQENFQKYASGVAKEVAEAGPRT 528
                                    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     |   -     | 390       400       410       420       430       440       450       460       470       480       490       500       510       520        
                                                                                                                                                                                                                                                                                                                                                                                                                 376       386
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PCKA_THET8 | Q5SLL5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCKA_THET8 | Q5SLL5: 1j3b 2pc9

(-) Related Entries Specified in the PDB File

1j3b SAME PROTEIN RELATED ID: TTK003000460.2 RELATED DB: TARGETDB