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(-) Description

Title :  X-RAY STRUCTURE OF THE DIHYDROXYACETONE KINASE FROM ESCHERICHIA COLI
 
Authors :  C. Siebold, L. -F. Garcia-Alles, B. Erni, U. Baumann
Date :  04 Jun 03  (Deposition) - 26 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Dihydroxyacetone Kinase, Ycgt (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Siebold, L. -F. Garcia-Alles, B. Erni, U. Baumann
A Mechanism Of Covalent Substrate Binding In The X-Ray Structure Of Subunit K Of The Escherichia Coli Dihydroxyacetone Kinase
Proc. Natl. Acad. Sci. Usa V. 100 8188 2003
PubMed-ID: 12813127  |  Reference-DOI: 10.1073/PNAS.0932787100

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YCGT
    Chains: A, B
    EC Number: 2.7.1.29
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WA2127
    Expression System Taxid: 562
    Expression System Vector: PMSEH2
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: COVALENTLY BOUND DIHYDROXYACETONE
    Synonym: DIHYDROXYACETONE KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:32 , HIS A:33 , PRO A:34 , SER A:35 , HOH A:2237 , HOH A:2238BINDING SITE FOR RESIDUE SO4 A1370
2AC2SOFTWAREHIS B:33 , PRO B:34 , SER B:35 , HOH B:2010BINDING SITE FOR RESIDUE SO4 B1370
3AC3SOFTWAREGLY A:62 , GLY A:63 , HIS A:66 , PHE A:88 , LYS A:114 , TYR A:116 , ASP A:119 , HIS A:230 , HOH A:2236BINDING SITE FOR RESIDUE GOL A1230
4AC4SOFTWAREGLY B:62 , GLY B:63 , HIS B:66 , PHE B:88 , LYS B:114 , TYR B:116 , ASP B:119 , HIS B:230 , HOH B:2252BINDING SITE FOR RESIDUE GOL B1230

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OI2)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asp A:41 -Pro A:42
2Ala A:50 -Pro A:51
3Glu A:67 -Pro A:68
4Met A:69 -His A:70
5Asp B:41 -Pro B:42
6Ala B:50 -Pro B:51
7Glu B:67 -Pro B:68
8Met B:69 -His B:70

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OI2)

(-) Exons   (0, 0)

(no "Exon" information available for 1OI2)

(-) Sequences/Alignments

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:336
 aligned with DHAK_ECOLI | P76015 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:347
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
           DHAK_ECOLI    10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
               SCOP domains d1oi2a_ A: Dihydroxyacetone kinase subunit K, DhaK                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1oi2A01 A:21-193 Dihydroxyacetone kinase; domain 1                                                                                                                           1oi2A02 A:1           94-368 Dihydroxyacetone kinase; domain 2                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhh.......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee..-----------....eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi2 A  20 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGAC-----------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 368
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199    |    -      |221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       
                                                                                                                                                                                                                  204         218                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with DHAK_ECOLI | P76015 from UniProtKB/Swiss-Prot  Length:356

    Alignment length:347
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
           DHAK_ECOLI    10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
               SCOP domains d1oi2b_ B: Dihydroxyacetone kinase subunit K, DhaK                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1oi2B01 B:21-193 Dihydroxyacetone kinase; domain 1                                                                                                                           1oi2B02 B:1           94-368 Dihydroxyacetone kinase; domain 2                                                                                                                CATH domains
           Pfam domains (1) ------Dak1-1oi2B01 B:26-368                                                                                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ------Dak1-1oi2B02 B:26-368                                                                                                                                                                                                                                                                                                                                 Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhh.......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eeeeeeeee..-----------....eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi2 B  20 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGAC-----------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 368
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199    |    -      |221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       
                                                                                                                                                                                                                  204         218
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: EDD (22)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DHAK_ECOLI | P76015)
molecular function
    GO:0004371    glycerone kinase activity    Catalysis of the reaction: ATP + glycerone = ADP + glycerone phosphate + 2 H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0047324    phosphoenolpyruvate-glycerone phosphotransferase activity    Catalysis of the reaction: glycerone + phosphoenolpyruvate = glycerone phosphate + pyruvate.
    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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0019563    glycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0042182    ketone catabolic process    The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
    GO:0046365    monosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of monosaccharides, polyhydric alcohols containing either an aldehyde or a keto group and between three to ten or more carbon atoms.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAK_ECOLI | P76015: 1oi3 1uod 1uoe 3pnk 3pnl 3pnm 3pno 3pnq 4lrx 4lry

(-) Related Entries Specified in the PDB File

1oi3 X-RAY STRUCTURE OF THE DIHYDROXYACETONE KINASE FROM ESCHERICHIA COLI