2J0X - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH LYSINE AND ASPARTATE (T-STATE)

Authors :   M. Kotaka, J. Ren, M. Lockyer, A. R. Hawkins, D. K. Stammers

Date :   07 Aug 06 (Deposition) - 10 Aug 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Feedback Inhibition, Allosteric Regulation, Aspartokinase, Aspartate Pathway, Lysine Biosynthesis, Lysine, Kinase, Act Domain, Transferase, Amino Acid Biosynthesis, Amino-Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kotaka, J. Ren, M. Lockyer, A. R. Hawkins, D. K. Stammers
Structures Of R- And T-State Escherichia Coli Aspartokinase Iii: Mechanisms Of The Allosteric Transition And Inhibition By Lysine.
J. Biol. Chem. V. 281 31544 2006
PubMed-ID: 16905770 | Reference-DOI: 10.1074/JBC.M605886200

Molecule 1 - LYSINE-SENSITIVE ASPARTOKINASE 3
	Chains	:	A, B
	EC Number	:	2.7.2.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	LYSINE-SENSITIVE ASPARTOKINASE III, ASPARTATE KINASE III

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ASP	1	Mod. Amino Acid	ASPARTIC ACID
2	LYS	2	Mod. Amino Acid	LYSINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS B:8 , GLY B:10 , GLY B:11 , SER B:39	BINDING SITE FOR RESIDUE PO4 A1000
2	AC2	SOFTWARE	SER A:39 , PHE A:184 , ARG A:198 , GLY A:199 , GLY A:200 , SER A:201 , ASP A:202 , HOH A:2051	BINDING SITE FOR RESIDUE ASP A 502
3	AC3	SOFTWARE	MET A:318 , SER A:321 , GLY A:323 , PHE A:324 , LEU A:325 , SER A:345 , GLU A:346 , HOH A:2039 , SER B:338 , VAL B:339 , ASP B:340	BINDING SITE FOR RESIDUE LYS A1451
4	AC4	SOFTWARE	SER A:338 , VAL A:339 , ASP A:340 , MET B:318 , SER B:321 , GLY B:323 , PHE B:324 , LEU B:325 , SER B:345	BINDING SITE FOR RESIDUE LYS B1450

(no "SS Bond" information available for 2J0X)

(no "Cis Peptide Bond" information available for 2J0X)

(no "SAP(SNP)/Variant" information available for 2J0X)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ASPARTOKINASE	PS00324	Aspartokinase signature.	AK3_ECOLI	6-14	2	A:6-14 B:6-14
2	ACT	PS51671	ACT domain profile.	AK3_ECOLI	313-394	2	A:313-394 B:313-394

(no "Exon" information available for 2J0X)

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:449
 aligned with AK3_ECOLI | P08660 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        449  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442      |  
           AK3_ECOLI      3 EIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFE--    -
               SCOP domains d2j0xa1 A:3-294 Aspartokinase                                                                                                                                                                                                                                                                       d2j0xa2 A:295-385 Aspartokinase                                                            d2j0xa3 A:386-449 Aspartokinase                                 -- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhh.ee.........hhhhhhhhhhhhhhhhhhhheeeee..eeee....eee...hhhhhhhhhhhhhh...eeeeee....................eeehhhhhhhhhhhhhh.hhhhhhhhhhh...eeeee..hhhhh.eeee........eeeeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh..eeeeeee...eeeeeee............hhhhhhhhhh..eeeeeeeeeeeeeee.........hhhhhhhhh.....eeee.....eeeeeeehhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ASPARTOKI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:313-394 UniProt: 313-394                                              --------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j0x A    3 EIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFEDK 1451
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442      |||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        449||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         502|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1451

Chain B from PDB  Type:PROTEIN  Length:446
 aligned with AK3_ECOLI | P08660 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         449 
                                    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       | 
           AK3_ECOLI      2 SEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFE-    -
               SCOP domains d2j0xb1 B:2-294 Aspartokinase                                                                                                                                                                                                                                                                        d2j0xb2 B:295-385 Aspartokinase                                                            d2j0xb3 B:386-449 Aspartokinase                                 - SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhh.ee.........hhhhhhhhhhhhhhhhhhhheeeee..eeee....eee...hhhhhhhhhhhhhh...eeeeee....................eeehhhhhhhhhhhhh..hhhhhhhhhhh...eeeee........eeee........eeeeeeeeeeeeeeee.hhhh...hhhhhhhhhhhhh..eeeeeee...eeeeeee.....---....hhhhhhhhhh..eeeeeeeeeeeeeee.........hhhhhhhhh.....eeee.....eeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ASPARTOKI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: B:313-394 UniProt: 313-394                                              -------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2j0x B    2 SEIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGST---DTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFEK 1450
                                    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       | - |     371       381       391       401       411       421       431       441       ||
                                                                                                                                                                                                                                                                                                                                                                                               359 363                                                                                   449|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1450

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: ACT-like (63)

Family: Aspartokinase allosteric domain-like (4)

Protein domain: Aspartokinase (4)

Escherichia coli [TaxId: 562] (2)

1a	d2j0xa2	A:295-385
1b	d2j0xa3	A:386-449
1c	d2j0xb2	B:295-385
1d	d2j0xb3	B:386-449

Class: Alpha and beta proteins (a/b) (23833)

Fold: Carbamate kinase-like (63)

Superfamily: Carbamate kinase-like (63)

Family: PyrH-like (22)

Protein domain: Aspartokinase (4)

Escherichia coli [TaxId: 562] (2)

2a	d2j0xa1	A:3-294
2b	d2j0xb1	B:2-294

(no "CATH Domain" information available for 2J0X)

(no "Pfam Domain" information available for 2J0X)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (AK3_ECOLI | P08660)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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: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:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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: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:0009090	homoserine biosynthetic process	The chemical reactions and pathways resulting in the formation of homoserine, alpha-amino-gamma-hydroxybutyric acid.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	AK3_ECOLI \| P08660	:	1ohi 2j0w

1ohi	MODELLED STRUCTURE OF ASPARTOKINASE III FROM ESCHERICHIA COLI
2j0w	CRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH ASPARTATE AND ADP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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