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(-) Description

Title :  APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (ORTHORHOMBIC SPACE GROUP)
 
Authors :  M. Schacherl, S. M. Waltersperger, U. Baumann
Date :  24 Mar 13  (Deposition) - 27 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Askha Superfamily, Phosphotransfer, Pseudomurein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Schacherl, S. M. Waltersperger, U. Baumann
Structural Characterization Of The Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 From Methanopyrus Kandleri
Acta Crystallogr. , Sect. D V. 69 2440 2013
PubMed-ID: 24311585  |  Reference-DOI: 10.1107/S0907444913022683

(-) Compounds

Molecule 1 - PREDICTED MOLECULAR CHAPERONE DISTANTLY RELATED TO HSP70-F OLD METALLOPROTEASES
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 190192
    Other Details: DSM6324
    Strain: AV19
    Synonym: PUTATIVE SUGAR KINASE MK0840

 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, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3K3Ligand/IonPOTASSIUM ION
4MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3K-1Ligand/IonPOTASSIUM ION
4MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:138 , ALA A:142 , PHE A:182 , GLY A:183 , ALA A:185 , SER A:243BINDING SITE FOR RESIDUE K A1351
2AC2SOFTWAREASP A:114 , ASP A:138 , GLY A:141 , PRO A:143 , ASP A:144 , HOH A:2046BINDING SITE FOR RESIDUE K A1352
3AC3SOFTWAREARG A:66 , GLU A:67 , SER A:310 , GLU A:311 , TRP A:313 , HOH A:2138BINDING SITE FOR RESIDUE K A1353
4AC4SOFTWAREGLU A:324 , ARG A:328 , HOH A:2144BINDING SITE FOR RESIDUE CL A1354
5AC5SOFTWAREVAL A:64 , ALA A:65 , ARG A:98 , ARG A:101 , VAL A:102 , ARG A:307 , ARG A:308 , GLU A:311BINDING SITE FOR RESIDUE ACT A1355

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BG9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:142 -Pro A:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BG9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BG9)

(-) Exons   (0, 0)

(no "Exon" information available for 4BG9)

(-) 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:315
 aligned with Q8TX37_METKA | Q8TX37 from UniProtKB/TrEMBL  Length:358

    Alignment length:315
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346     
         Q8TX37_METKA    37 LTRVLGIQLGNTGTDYCVMNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPMIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAMAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDMDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee....eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhh..eeeeee..eeeeeeee..ee.....eeee.hhhhhhhhhhhhh........hhhhh..hhhhhhhhhh.ee..ee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhh.....eeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bg9 A  37 LTRVLGIQLGNTGTDYCVmNEDGDWEIVAREEGVFGKISCVFTLEESRRALREEIAPRVIERVRRVNPDLAVVGTIVDELGLILGPmIHEKTGVPTLAVYGDPWGAPDGDAVGAPYCVAEEYPNCVHVDVGAmAVVTPIRDGRPDFGDAVVSVGTFPLDLAARELLGKEYDEGGKKAAEGEVDENFRRELRSVDVDGKPVFGRVRGSLAPVPPEQERVLRDHIRDAGAPAEDVLRTLVELVAETIVINAAQYDmDLLVLSGGGVKNELLKRRVSELWEGDVSIFAGEELEARGLCLLGLRYLEGEPVPALPCEGG 351
                                    46        56        66        76        86        96       106       116      |126       136       146       156       166  |    176       186       196       206       216       226       236       246       256       266       276       286   |   296       306       316       326       336       346     
                                             55-MSE                                                             123-MSE                                       169-MSE                                                                                                                  290-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  (0, 0)

(no "SCOP Domain" information available for 4BG9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BG9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BG9)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8TX37_METKA | Q8TX37)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
biological process
    GO:0006040    amino sugar metabolic process    The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.
    GO:0009254    peptidoglycan turnover    The continual breakdown and regeneration of peptidoglycan required to maintain the cell wall.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8TX37_METKA | Q8TX37: 4bg8 4bga 4bgb

(-) Related Entries Specified in the PDB File

4bg8 APO FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI (MONOCLINIC SPACE GROUP)
4bga NUCLEOTIDE-BOUND OPEN FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI
4bgb NUCLEOTIDE-BOUND CLOSED FORM OF A PUTATIVE SUGAR KINASE MK0840 FROM METHANOPYRUS KANDLERI