Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH ASPARTATE AND ADP (R-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 :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Feedback Inhibition, Allosteric Regulation, Kinase, Act Domain, Transferase, Aspartokinase, Amino Acid Biosynthesis, Amino-Acid Biosynthesis, Aspartate Pathway, Lysine 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

(-) Compounds

Molecule 1 - LYSINE-SENSITIVE ASPARTOKINASE 3
    ChainsA
    EC Number2.7.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymASPARTOKINASE III, LYSINE-SENSITIVE ASPARTOKINASE III, ASPARTATE KINASE III

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ASP1Mod. Amino AcidASPARTIC ACID
3CL1Ligand/IonCHLORIDE ION
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2ASP2Mod. Amino AcidASPARTIC ACID
3CL-1Ligand/IonCHLORIDE ION
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:43 , THR A:45 , ASN A:46BINDING SITE FOR RESIDUE CL A 600
2AC2SOFTWAREASP A:202 , ADP A:820 , HOH A:2038 , HOH A:2039 , HOH A:2067 , HOH A:2068BINDING SITE FOR RESIDUE MG A 900
3AC3SOFTWARESER A:39 , THR A:45 , GLU A:119 , PHE A:184 , ARG A:198 , GLY A:199 , GLY A:200 , SER A:201 , HOH A:2001 , HOH A:2038 , HOH A:2068BINDING SITE FOR RESIDUE ASP A 502
4AC4SOFTWARELYS A:8 , GLY A:10 , GLY A:11 , THR A:221 , ASP A:222 , VAL A:223 , GLY A:225 , TYR A:227 , ASP A:230 , ARG A:232 , MET A:251 , LYS A:257 , VAL A:258 , MG A:900 , HOH A:2001 , HOH A:2067 , HOH A:2068BINDING SITE FOR RESIDUE ADP A 820

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J0W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J0W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J0W)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASPARTOKINASEPS00324 Aspartokinase signature.AK3_ECOLI6-14  1A:6-14
2ACTPS51671 ACT domain profile.AK3_ECOLI313-394  1A:313-394
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASPARTOKINASEPS00324 Aspartokinase signature.AK3_ECOLI6-14  2A:6-14
2ACTPS51671 ACT domain profile.AK3_ECOLI313-394  2A:313-394

(-) Exons   (0, 0)

(no "Exon" information available for 2J0W)

(-) 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:448
 aligned with AK3_ECOLI | P08660 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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 d2j0wa1 A:3-294 Aspartokinase                                                                                                                                                                                                                                                                       d2j0wa2 A:295-385 Aspartokinase                                                            d2j0wa3 A:386-449 Aspartokinase                                 - SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhh............hhhhhhhhhhhhhhhhhhhheeeee..eee.....eee...hhhhhhhhhhhhhh...eeeeee....ee...........ee.eeehhhhhhhhhh........hhhhhhhhh..eeeee........eeee........eeeeeeeeeeeeeee......hhhhhhhhhh...........eeeee..eeeeee.............hhhhhhhhhhhh.eeeeeeeeeeeeee.......hhhhhhhh........eee......eeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ASPARTOKI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACT  PDB: A:313-394 UniProt: 313-394                                              -------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j0w A   3 EIVVSKFGGTSVADFDAMNRSADIVLSDANVRLVVLSASAGITNLLVALAEGLEPGERFEKLDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELVSHGELMSTLLFVEILRERDVQAQWFDVRKVMRTNDRFGRAEPDIAALAELAALQLLPRLNEGLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSAAKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKTENPPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDTTGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNIRMICYGASSHNLCFLVPGEDAEQVVQKLHSNLFED 502
                                    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

   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, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J0W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J0W)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ASP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2j0w)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2j0w
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AK3_ECOLI | P08660
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.2.4
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  AK3_ECOLI | P08660
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        AK3_ECOLI | P086601ohi 2j0x

(-) Related Entries Specified in the PDB File

1ohi MODELLED STRUCTURE OF ASPARTOKINASE III FROM ESCHERICHIA COLI
2j0x CRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH LYSINE AND ASPARTATE (T-STATE)