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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI DHA KINASE DHAK-DHAL COMPLEX
 
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) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Dha Kinase, 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
    ChainsA
    EC Number2.7.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneB1200, DHAK, JW5187, YCGT
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12
 
Molecule 2 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, ADP-BINDING SUBUNIT DHAL
    ChainsB
    EC Number2.7.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneB1199, DHAL, JW5186, YCGS
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK-12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB
Biological Unit 2 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:52 , GLY A:53 , HIS A:56 , PHE A:78 , SER A:80 , LYS A:104 , ASP A:109 , HIS A:218 , ARG B:178 , HOH B:231BINDING SITE FOR RESIDUE GOL A 1228
2AC2SOFTWARETHR A:107 , HOH A:359 , ASP B:30 , ASP B:35 , ASP B:37 , HIS B:38 , ASN B:41 , GLY B:78 , ALA B:79 , SER B:80 , LEU B:83 , GLY B:121 , THR B:129 , MET B:130 , GLY B:177 , ASP B:191 , PRO B:192 , GLY B:193 , HOH B:215 , HOH B:216 , HOH B:231 , HOH B:243 , HOH B:254 , MG B:1212 , MG B:1213BINDING SITE FOR RESIDUE ADP B 1211
3AC3SOFTWAREASP B:30 , ASP B:35 , ASP B:37 , HOH B:254 , ADP B:1211 , MG B:1213BINDING SITE FOR RESIDUE MG B 1212
4AC4SOFTWAREPHE A:78 , ASP B:35 , ASP B:37 , HOH B:231 , ADP B:1211 , MG B:1212BINDING SITE FOR RESIDUE MG B 1213

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHALPS51480 DhaL domain profile.DHAL_ECOLI6-206  1B:6-206
2DHAKPS51481 DhaK domain profile.DHAK_ECOLI7-352  1A:7-352
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHALPS51480 DhaL domain profile.DHAL_ECOLI6-206  2B:6-206
2DHAKPS51481 DhaK domain profile.DHAK_ECOLI7-352  2A:7-352
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHALPS51480 DhaL domain profile.DHAL_ECOLI6-206  1B:6-206
2DHAKPS51481 DhaK domain profile.DHAK_ECOLI7-352  1A:7-352

(-) Exons   (0, 0)

(no "Exon" information available for 3PNL)

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

    Alignment length:356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      
           DHAK_ECOLI     1 MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
               SCOP domains d3pnla_ A: automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------Dak1-3pnlA01 A:16-356                                                                                                                                                                                                                                                                                                                                 Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh....eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee.................eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeeeehhhhhhhhhh.ee....ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------DHAK  PDB: A:7-352 UniProt: 7-352                                                                                                                                                                                                                                                                                                                         ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnl A   1 SKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      

Chain B from PDB  Type:PROTEIN  Length:211
 aligned with DHAL_ECOLI | P76014 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:211
                             1                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           DHAL_ECOLI     - -MSLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE 210
               SCOP domains d3pnlb_ B: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------Dak2-3pnlB01 B:32-206                                                                                                                                                          ---- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------DHAL  PDB: B:6-206 UniProt: 6-206                                                                                                                                                                        ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnl B   0 GSSLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE 210
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: EDD (22)

(-) Gene Ontology  (17, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

Chain B   (DHAL_ECOLI | P76014)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) 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: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.
    GO:0016772    transferase activity, transferring phosphorus-containing groups    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
biological process
    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: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 | P760151oi2 1oi3 1uod 1uoe 3pnk 3pnm 3pno 3pnq 4lrx 4lry
        DHAL_ECOLI | P760142btd 4lrz

(-) Related Entries Specified in the PDB File

3pnk 3pnm 3pno 3pnq