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(-) Description

Title :  STRUCTURE OF AN ESCHERICHIA COLI LIPID KINASE (YEGS)
 
Authors :  H. M. Bakali, K. A. Johnson, B. M. Hallberg, M. D. Herman, P. Nordlund
Date :  12 Apr 05  (Deposition) - 18 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dag Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Bakali, M. D. Herman, K. A. Johnson, A. A. Kelly, A. Wieslander, B. M. Hallberg, P. Nordlund
Crystal Structure Of Yegs, A Homologue To The Mammalian Diacylglycerol Kinases, Reveals A Novel Regulatory Metal Binding Site.
J. Biol. Chem. V. 282 19644 2007
PubMed-ID: 17351295  |  Reference-DOI: 10.1074/JBC.M604852200

(-) Compounds

Molecule 1 - LIPID KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: GATEWAY
    Organism Common: ESCHERICHIA COLI
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 469008
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:215 , ASP A:218 , LEU A:220 , HOH A:2007 , HOH A:2018 , HOH A:2024BINDING SITE FOR RESIDUE MG A1302
2AC2SOFTWARELEU B:215 , ASP B:218 , LEU B:220 , HOH B:2025 , HOH B:2026 , HOH B:2030BINDING SITE FOR RESIDUE MG B1302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BON)

(-) 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:287
 aligned with YEGS_ECOLI | P76407 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:297
                                                                                                                                                                                                                                                                                                                                299  
                                    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    |  
           YEGS_ECOLI     5 PASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDMAQVNKQTCFINMATGGFGTRITTETPEKLKAALGSVSYIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFTGDEILPALVSTLKSDEDNPNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLR--   -
               SCOP domains d2bona1 A:5-299 Lipid kinase YegS                                                                                                                                                                                                                                                                      -- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh......eeeeee....hhhhhhh....hhhhhhhhhhhheeeeeeeeee....ee..eeeeeeeee.----------.hhhhhhhhhhh........eeeeeee..eeeeeee......................................hhhhhhhhhh.............eeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bon A   5 PASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDMAQVNKQTCFINMATGGFGTRI----------ALGSVSYIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFTGDEILPALVSTLKSDEDNPNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLRST 301
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  |      -   |   164       174       184       194       204       214       224       234       244       254       264       274       284       294       
                                                                                                                                                                        147        158                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with YEGS_ECOLI | P76407 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:297
                                                                                                                                                                                                                                                                                                                                299  
                                    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    |  
           YEGS_ECOLI     5 PASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDMAQVNKQTCFINMATGGFGTRITTETPEKLKAALGSVSYIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFTGDEILPALVSTLKSDEDNPNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLR--   -
               SCOP domains d2bonb_ B: Lipid kinase YegS                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhh.......eeeee.....hhhhhhh....hhhhhhhhhhhh.eeeeeeeee...eee..eeeee.....--------------hhhhhh..........eeeeeee..eeeeeee.eeeee.....................eeeeee.------------------..eeeeee.eeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bon B   5 PASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDMAQVNKQTCFINMATGGFGTRI--------------VSYIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFT------------------PNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLRST 301
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144  |      -       164       174       184       194       204       214       224  |      -         - |     254       264       274       284       294       
                                                                                                                                                                        147            162                                                              227                246
   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, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YEGS_ECOLI | P76407)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0001727    lipid kinase activity    Catalysis of the phosphorylation of a simple or complex lipid.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0046834    lipid phosphorylation    The process of introducing one or more phosphate groups into a lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        YEGS_ECOLI | P76407: 2jgr

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