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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTATE KINASE FROM SYNECHOCYSTIS
 
Authors :  A. Robin, D. Cobessi, G. Curien, M. Robert-Genthon, J. -L. Ferrer, R. Du
Date :  28 Dec 09  (Deposition) - 09 Jun 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aspartokinase, Synechocystis, Allostery, Act Domains, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Y. Robin, D. Cobessi, G. Curien, M. Robert-Genthon, J. -L. Ferrer, R. Dumas
A New Mode Of Dimerization Of Allosteric Enzymes With Act Domains Revealed By The Crystal Structure Of The Aspartate Kinase From Cyanobacteria
J. Mol. Biol. V. 399 283 2010
PubMed-ID: 20398676  |  Reference-DOI: 10.1016/J.JMB.2010.04.014

(-) Compounds

Molecule 1 - ASPARTOKINASE
    Chains: A, B
    EC Number: 2.7.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LYSC, SLR0657
    Organism Scientific: SYNECHOCYSTIS
    Organism Taxid: 1148
    Strain: PCC 6803
    Synonym: ASPARTATE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1LYS4Mod. Amino AcidLYSINE
2SO41Ligand/IonSULFATE ION
3THR4Mod. Amino AcidTHREONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:280 , ARG A:281 , PRO A:282 , GLY A:283 , VAL A:284 , ALA A:285 , GLN A:304 , ASN A:557 , ILE A:558 , HOH A:630 , HOH A:631BINDING SITE FOR RESIDUE THR A 601
2AC2SOFTWAREASN A:385 , ILE A:386 , ASP A:454 , ARG A:455 , GLY A:457 , MET A:458 , ALA A:459 , GLN A:478 , HOH A:613BINDING SITE FOR RESIDUE THR A 602
3AC3SOFTWAREASP A:298 , ILE A:299 , ASP A:300 , MET A:537 , HIS A:540 , GLY A:542 , VAL A:543 , ALA A:544 , THR A:563 , SER A:564 , ILE A:568 , HOH A:614 , HOH A:674 , HOH A:691BINDING SITE FOR RESIDUE LYS A 603
4AC4SOFTWAREMET A:365 , ARG A:368 , GLY A:370 , ILE A:371 , ALA A:372 , SER A:392 , GLU A:393 , SER A:472 , VAL A:473 , ASP A:474 , HOH A:607 , HOH A:609 , HOH A:624 , HOH A:687BINDING SITE FOR RESIDUE LYS A 604
5AC5SOFTWAREARG A:277 , ASP A:308 , ASN A:310 , SER A:311 , ARG A:483BINDING SITE FOR RESIDUE SO4 A 605
6AC6SOFTWAREASN B:385 , ILE B:386 , VAL B:452 , ASP B:454 , ARG B:455 , MET B:458 , ALA B:459 , GLN B:478 , ILE B:493 , HOH B:617BINDING SITE FOR RESIDUE THR B 601
7AC7SOFTWAREASP B:280 , ARG B:281 , PRO B:282 , GLY B:283 , VAL B:284 , ALA B:285 , GLN B:304 , ASN B:557 , ILE B:558BINDING SITE FOR RESIDUE THR B 602
8AC8SOFTWAREASP B:298 , ILE B:299 , ASP B:300 , MET B:537 , HIS B:540 , PRO B:541 , GLY B:542 , VAL B:543 , ALA B:544 , THR B:563 , SER B:564 , ILE B:568 , HOH B:623 , HOH B:649BINDING SITE FOR RESIDUE LYS B 603
9AC9SOFTWAREMET B:365 , ARG B:368 , PRO B:369 , GLY B:370 , ILE B:371 , ALA B:372 , SER B:392 , GLU B:393 , SER B:472 , VAL B:473 , ASP B:474 , HOH B:611 , HOH B:651BINDING SITE FOR RESIDUE LYS B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L76)

(-) Exons   (0, 0)

(no "Exon" information available for 3L76)

(-) 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:589
 aligned with P74569_SYNY3 | P74569 from UniProtKB/TrEMBL  Length:600

    Alignment length:603
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                600    
                                    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       531       541       551       561       571       581       591        |-   
         P74569_SYNY3     2 ALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPNPCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDRLEHHLREGKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGTKVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGVTLSPPKNQTDTSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDMIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGSGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKTVTVPA----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeee.-------..eeee.hhhhhhh...eeeee.eee.----.eeee....hhhhhhhhhhhhhhh..eeeeee....................eeehhhhhhhhhhhh...hhhhhhhhhhhh..eeeee.......eeee...................eeeee...eeeeeeeee...hhhhhhhhhhhhh......ee.......eeeeeeeehhhhhhhhhhhhhhhhhhhh.........eeeee..eeeeeee.hhhh...hhhhhhhhhhhhh.....eeee...eeeeeee..hhhhhhhhhhhhh............---.....eeeee..eeeeeeeeee...hhhhhhhhhhhhh.....eeeeeee........eeeeeeeeehhhhhhhhhhhhhhh......eeeee..eeeeeee.hhhh...hhhhhhhhhhhh......eeee...eeeeeee..hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l76 A   2 ALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPNPCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTE-------ILEIRPDRLEHHLREGKVVVVAGFQGI----HLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGTKVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGVTLSPPKNQTD---LPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDMIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGSGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKTVTVPATTKK 604
                                    11        21        31        41        51        61        71        81        91       101   |     - |     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       381       391       401       411       421      |  -|      441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601   
                                                                                                                                 105     113                       139  144                                                                                                                                                                                                                                                                                         428 432                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:585
 aligned with P74569_SYNY3 | P74569 from UniProtKB/TrEMBL  Length:600

    Alignment length:603
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                600    
                                    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       531       541       551       561       571       581       591        |-   
         P74569_SYNY3     2 ALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPNPCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTEAEHSRARILEIRPDRLEHHLREGKVVVVAGFQGISSVEHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGTKVVAPPVQNRSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGVTLSPPKNQTDTSHLPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDMIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGSGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKTVTVPA----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) AA_kinase-3l76B09 B:2-232                                                                                                                                                                                                              ---------------  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      ---------------------------------------------------------------------------------------------------ACT-3l76B01 B:531-589                                      --------------- Pfam domains (1)
           Pfam domains (2) AA_kinase-3l76B10 B:2-232                                                                                                                                                                                                              ---------------  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------      ---------------------------------------------------------------------------------------------------ACT-3l76B02 B:531-589                                      --------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B03 B:531-589                                      --------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B04 B:531-589                                      --------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B05 B:531-589                                      --------------- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B06 B:531-589                                      --------------- Pfam domains (6)
           Pfam domains (7) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B07 B:531-589                                      --------------- Pfam domains (7)
           Pfam domains (8) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT-3l76B08 B:531-589                                      --------------- Pfam domains (8)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeee.--------.eeee.hhhhhhh...eeeee.eeee.--..eeee....hhhhhhhhhhhhhh...eeeeee....................eeehhhhhhhhhhhh...hhhhhhhhhhh...eeeee.......eeee....--.....ee......eeeeeeeeeeeeeeeee...hhhhhhhhhhhhh......ee.......eeeeeeeehhhhhhhhhhhhhhhhhhhh.........eeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh.....eeee...eeeeeee..hhhhhhhhhhhhh.........------.....eeeee..eeeeeeeeee...hhhhhhhhhhhhh.....eeeeeee........eeeeeeeeehhhhhhhhhhhhhhhh.....eeeee..eeeeeee.hhhh...hhhhhhhhhhhh......eeee...eeeeeee..hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l76 B   2 ALIVQKFGGTSVGTVERIQAVAQRIKRTVQGGNSLVVVVSAMGKSTDVLVDLAQQISPNPCRREMDMLLSTGEQVSIALLSLALQEIDQPAISLTGAQVGIVTE--------LEIRPDRLEHHLREGKVVVVAGFQGIS--EHLEITTLGRGGSDTSAVALAAALKADFCEIYTDVPGILTTDPRLVPEAQLMAEITCDEMLELASLGAKVLHPRAVEIARNYGIPLVVRSSWSDEPGTKVVAPPV--RSLVGLEIAKAVDGVEYDADQAKVALLRVPDRPGVASKLFRDIAQQQVDIDLIIQSIHDGNSNDIAFTVVKDLLNTAEAVTSAIAPALRSYPEADQEAEIIVEKGIAKIAIAGAGMIGRPGIAAKMFKTLADVGVNIEMISTSEVKVSCVIDQRDADRAIAALSNAFGVTLSPPKN------LPAVRGVALDQDQAQIAIRHVPDRPGMAAQLFTALAEANISVDMIIQSQRCRINQGTPCRDIAFMVAEGDSSQAEAILQPLIKDWLDAAIVVNKAIAKVSIVGSGMIGHPGVAAHFFAALAQENINIEMIATSEIKISCVVPQDRGVDALKAAHSAFNLAGTKTVTVPATTKK 604
                                    11        21        31        41        51        61        71        81        91       101   |     -  |    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       381       391       401       411       421   |     -|      441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601   
                                                                                                                                 105      114                       140  |                                                                                                     247  |                                                                                                                                                                            425    432                                                                                                                                                                            
                                                                                                                                                                       143                                                                                                        250
   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  (0, 0)

(no "SCOP Domain" information available for 3L76)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L76)

(-) Pfam Domains  (2, 10)

Asymmetric/Biological Unit
(-)
Clan: ACT (34)
(-)
Family: ACT (19)
(-)
Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) (1)
1aACT-3l76B01B:531-589
1bACT-3l76B02B:531-589
1cACT-3l76B03B:531-589
1dACT-3l76B04B:531-589
1eACT-3l76B05B:531-589
1fACT-3l76B06B:531-589
1gACT-3l76B07B:531-589
1hACT-3l76B08B:531-589
(-)
Clan: no clan defined [family: AA_kinase] (20)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P74569_SYNY3 | P74569)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0004072    aspartate kinase activity    Catalysis of the reaction: L-aspartate + ATP = 4-phospho-L-aspartate + ADP + H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    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.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  3l76
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  P74569_SYNY3 | P74569
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 Related Entries

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