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(-) Description

Title :  CRYSTAL STRUCTURE OF DHAL FROM E. COLI
 
Authors :  A. E. Oberholzer, P. Schneider, C. Bachler, U. Baumann, B. Erni
Date :  27 May 05  (Deposition) - 22 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Dihydroxiacetone Kinase, Dhal, Ycgs, Pts, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. E. Oberholzer, P. Schneider, U. Baumann, B. Erni
Crystal Structure Of The Nucleotide-Binding Subunit Dhal Of The Escherichia Coli Dihydroxyacetone Kinase.
J. Mol. Biol. V. 359 539 2006
PubMed-ID: 16647083  |  Reference-DOI: 10.1016/J.JMB.2006.03.057

(-) Compounds

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE
    Chains: A
    EC Number: 2.7.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector: PJF H6
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ADP-BINDING SUBUNIT DHAL, DHAL

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:30 , ASP A:35 , ASP A:37 , ADP A:1211 , HOH A:2008BINDING SITE FOR RESIDUE MG A1212
2AC2SOFTWAREASP A:35 , ASP A:37 , ADP A:1211BINDING SITE FOR RESIDUE MG A1213
3AC3SOFTWAREASP A:30 , ASP A:35 , ASP A:37 , HIS A:38 , ASN A:41 , GLY A:78 , ALA A:79 , SER A:80 , LEU A:83 , GLY A:121 , THR A:129 , MET A:130 , GLY A:177 , ARG A:178 , ASP A:191 , PRO A:192 , GLY A:193 , ALA A:194 , MG A:1212 , MG A:1213 , HOH A:2008 , HOH A:2038 , HOH A:2039BINDING SITE FOR RESIDUE ADP A1211

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHALPS51480 DhaL domain profile.DHAL_ECOLI6-206  1A:6-206

(-) Exons   (0, 0)

(no "Exon" information available for 2BTD)

(-) 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:209
 aligned with DHAL_ECOLI | P76014 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:209
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           DHAL_ECOLI     2 SLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE 210
               SCOP domains d2btda_ A: automated matches                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DHAL  PDB: A:6-206 UniProt: 6-206                                                                                                                                                                        ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2btd A   2 SLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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
        DHAL_ECOLI | P76014: 3pnl 4lrz

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