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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMOSERINE KINASE FROM AGROBACTERIUM TUMEFACIENS
 
Authors :  R. Zhang, X. Xu, H. Zheng, A. Savchenko, A. Edwards, A. Joachimiak, Midw Center For Structural Genomics (Mcsg)
Date :  30 Apr 07  (Deposition) - 05 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Homoserine Kinase, Structural Genomics, Mcsg, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, X. Xu, H. Zheng, A. Savchenko, A. Edwards, A. Joachimiak
The Crystal Structure Of The Homoserine Kinase From Agrobacterium Tumefaciens.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOMOSERINE KINASE
    Atcc: 33970
    Chains: A
    EC Number: 2.7.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDM68
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: THRB, ATU0775, AGR_C_1416
    Organism Scientific: AGROBACTERIUM TUMEFACIENS STR.
    Organism Taxid: 176299
    Strain: C58
    Synonym: HSK, HK

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:116 , ASP A:204 , GLU A:263BINDING SITE FOR RESIDUE MG A 323
2AC2SOFTWAREASP A:197 , ASN A:198 , ASP A:211 , HOH A:442 , HOH A:461BINDING SITE FOR RESIDUE PO4 A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PPQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PPQ)

(-) 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:310
 aligned with KHSE_AGRFC | Q8UHA8 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:316
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
           KHSE_AGRFC     5 TDITEDELRNFLTQYDVGSLTSYKGIAEGVENSNFLLHTTKDPLILTLYEKRVEKNDLPFFLGLMQHLAAKGLSCPLPLPRKDGELLGELSGRPAALISFLEGMWLRKPEAKHCREVGKALAAMHLASEGFEIKRPNALSVDGWKVLWDKSEERADEVEKGLREEIRPEIDYLAAHWPKDLPAGVIHADLFQDNVFFLGDELSGLIDFYFACNDLLAYDVSICLNAWCFEKDGAYNVTKGKALLEGYQSVRPLSEAELEALPLLSRGSALRFFLTRLYDWLTTPAGALVVKKDPLEYLRKLRFHRTIANVAEYGLA 320
               SCOP domains d2ppqa1 A:5-320 Homoserine    kinase ThrB                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2ppqA01 A:5-104 Phosphoryla   se Kinase; domain 1                                                   -2ppqA02 A:106-319  [code=3.90.1200.10, no name defined]                                                                                                                                                               - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh......eeeeeee.---.eeeeeeee....eeeeee..---.hhhhhhhhhhhhhhhh................eee..eeeeeee..........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....eeee....hhh.eeee..eeeee......eeeehhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ppq A   5 TDITEDELRNFLTQYDVGSLTSYKGIA---ENSNFLLHTTKDPLILTLYEK---KNDLPFFLGLmQHLAAKGLSCPLPLPRKDGELLGELSGRPAALISFLEGmWLRKPEAKHCREVGKALAAmHLASEGFEIKRPNALSVDGWKVLWDKSEERADEVEKGLREEIRPEIDYLAAHWPKDLPAGVIHADLFQDNVFFLGDELSGLIDFYFACNDLLAYDVSICLNAWCFEKDGAYNVTKGKALLEGYQSVRPLSEAELEALPLLSRGSALRFFLTRLYDWLTTPAGALVVKKDPLEYLRKLRFHRTIANVAEYGLA 320
                                    14        24      |  -|       44        54|   |   64    |   74        84        94       104   |   114       124   |   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314      
                                                     31  35                  55  59        69-MSE                                108-MSE             128-MSE
   Legend:   → Mismatch (orange background)
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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  (1, 1)

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

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (KHSE_AGRFC | Q8UHA8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004413    homoserine kinase activity    Catalysis of the reaction: L-homoserine + ATP = O-phospho-L-homoserine + ADP + 2 H(+).
    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: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.
    GO:0009088    threonine biosynthetic process    The chemical reactions and pathways resulting in the formation of threonine (2-amino-3-hydroxybutyric acid), a polar, uncharged, essential amino acid found in peptide linkage in proteins.

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