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(-) Description

Title :  DEPHOSPHO-COA KINASE IN COMPLEX WITH ATP
 
Authors :  G. Obmolova, A. Teplyakov, N. Bonander, E. Eisenstein, A. J. Howard, G. L. Gilliland, Structure 2 Function Project (S2F)
Date :  09 Jul 01  (Deposition) - 01 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Loop Nucleotide-Binding Fold, Structure 2 Function Project, S2F, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Obmolova, A. Teplyakov, N. Bonander, E. Eisenstein, A. J. Howard, G. L. Gilliland
Crystal Structure Of Dephospho-Coenzyme A Kinase From Haemophilus Influenzae.
J. Struct. Biol. V. 136 119 2001
PubMed-ID: 11886213  |  Reference-DOI: 10.1006/JSBI.2001.4428
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEPHOSPHO-COA KINASE
    Chains: A
    EC Number: 2.7.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET15B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YACE
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Synonym: DEPHOSPHOCOENZYME A KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2HG1Ligand/IonMERCURY (II) ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:93 , LYS A:97 , LYS A:167 , HOH A:437 , HOH A:502BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWARETHR A:121 , CYS A:124 , ARG A:126 , ILE A:127 , HOH A:382BINDING SITE FOR RESIDUE HG A 302
3AC3SOFTWAREILE A:11 , GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , THR A:16 , THR A:17 , ASN A:86 , ARG A:140 , ASN A:175 , ALA A:177 , GLU A:178 , LEU A:179 , HOH A:368 , HOH A:373 , HOH A:376 , HOH A:389 , HOH A:393 , HOH A:423BINDING SITE FOR RESIDUE ATP A 300

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JJV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPCKPS51219 Dephospho-CoA kinase (DPCK) domain profile.COAE_HAEIN4-204  1A:4-204

(-) Exons   (0, 0)

(no "Exon" information available for 1JJV)

(-) 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:194
 aligned with COAE_HAEIN | P44920 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
           COAE_HAEIN     1 MTYIVGLTGGIGSGKTTIANLFTDLGVPLVDADVVAREVVAKDSPLLSKIVEHFGAQILTEQGELNRAALRERVFNHDEDKLWLNNLLHPAIRERMKQKLAEQTAPYTLFVVPLLIENKLTALCDRILVVDVSPQTQLARSAQRDNNNFEQIQRIMNSQVSQQERLKWADDVINNDAELAQNLPHLQQKVLELHQFYLQQAENKN 205
               SCOP domains d1jjva_ A: Dephospho-CoA kinase                                                                                                                                                                               SCOP domains
               CATH domains 1jjvA00 A:1-205 P-loop containing nucleotide triphosphate       hydrolases                                                                                                                                    CATH domains
               Pfam domains --CoaE-1jjvA01 A:3-181                                                                                                                                                               ------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh....eeehhhhhhhh....hhhhhhhhhhhh...------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhh.eeeeee.hhhhhhhhhh-----hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: A:4-204 UniProt: 4-204                                                                                                                                                                        - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jjv A   1 MTYIVGLTGGIGSGKTTIANLFTDLGVPLVDADVVAREVVAKDSPLLSKIVEHFGAQI------LNRAALRERVFNHDEDKLWLNNLLHPAIRERMKQKLAEQTAPYTLFVVPLLIENKLTALCDRILVVDVSPQTQLARSA-----NFEQIQRIMNSQVSQQERLKWADDVINNDAELAQNLPHLQQKVLELHQFYLQQAENKN 205
                                    10        20        30        40        50       | -    |   70        80        90       100       110       120       130       140 |     150       160       170       180       190       200     
                                                                                    58     65                                                                          142   148
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (COAE_HAEIN | P44920)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004140    dephospho-CoA kinase activity    Catalysis of the reaction: 3'-dephospho-CoA + ATP = ADP + CoA + 2 H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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:0015937    coenzyme A biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
    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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