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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI DHA KINASE DHAK (H56N) COMPLEX WITH DHA
 
Authors :  R. Shi, L. Mcdonald, A. Matte, M. Cygler, I. Ekiel, Montreal-Kingston Structural Genomics Initiative (Bsgi)
Date :  19 Nov 10  (Deposition) - 12 Jan 11  (Release) - 16 Feb 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Shi, L. Mcdonald, Q. Cui, A. Matte, M. Cygler, I. Ekiel
Structural And Mechanistic Insight Into Covalent Substrate Binding By Escherichia Coli Dihydroxyacetone Kinase.
Proc. Natl. Acad. Sci. Usa V. 108 1302 2011
PubMed-ID: 21209328  |  Reference-DOI: 10.1073/PNAS.1012596108

(-) Compounds

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- BINDING SUBUNIT DHAK
    Chains: A, B, C, D
    EC Number: 2.7.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B1200, DHAK, JW5187, YCGT
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
12HA1Ligand/IonDIHYDROXYACETONE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
12HA-1Ligand/IonDIHYDROXYACETONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12HA1Ligand/IonDIHYDROXYACETONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY D:52 , GLY D:53 , PHE D:78 , SER D:80 , LYS D:104 , TYR D:106 , ASP D:109 , HIS D:218 , HOH D:549BINDING SITE FOR RESIDUE 2HA D 511

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PNQ)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Asp A:31 -Pro A:32
2Ala A:40 -Pro A:41
3Glu A:57 -Pro A:58
4Met A:59 -His A:60
5Asp B:31 -Pro B:32
6Ala B:40 -Pro B:41
7Glu B:57 -Pro B:58
8Met B:59 -His B:60
9Asp C:31 -Pro C:32
10Ala C:40 -Pro C:41
11Glu C:57 -Pro C:58
12Met C:59 -His C:60
13Asp D:31 -Pro D:32
14Ala D:40 -Pro D:41
15Glu D:57 -Pro D:58
16Met D:59 -His D:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PNQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PNQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3PNQ)

(-) 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:334
 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 d3pnqa_ A: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee-------------....eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnq A  10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALG-------------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  |      -      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
                                                                                                                                                                                                                192           206                                                                                                                                                      


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 d3pnqb_ B: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee..-----------....eeeeee........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnq B  10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGAC-----------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    |    -      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
                                                                                                                                                                                                                  194         206                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:335
 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 d3pnqc_ C: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeee...------------....eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee.........eeeeeeee.hhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnq C  10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGA------------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189   |     -      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
                                                                                                                                                                                                                 193          206                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:334
 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 d3pnqd_ D: automated matches                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------Dak1-3pnqD01 D:16-356                                                                                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) ------Dak1-3pnqD02 D:16-356                                                                                                                                                                                                                                                                                                                                 Pfam domains (2)
           Pfam domains (3) ------Dak1-3pnqD03 D:16-356                                                                                                                                                                                                                                                                                                                                 Pfam domains (3)
           Pfam domains (4) ------Dak1-3pnqD04 D:16-356                                                                                                                                                                                                                                                                                                                                 Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhh...eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee-------------....eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeee.hhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnq D  10 DVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALG-------------LADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  |      -      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       
                                                                                                                                                                                                                192           206
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PNQ)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: EDD (22)
(-)
Family: Dak1 (10)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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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  3pnq
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  DHAK_ECOLI | P76015
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  2.7.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAK_ECOLI | P76015: 1oi2 1oi3 1uod 1uoe 3pnk 3pnl 3pnm 3pno 4lrx 4lry

(-) Related Entries Specified in the PDB File

3pnk 3pnl 3pnm 3pno