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(-) Description

Title :  CRYSTAL STRUCTURE OF DEPHOSPHOCOENZYME A KINASE FROM ESCHERICHIA COLI
 
Authors :  N. O'Toole, J. A. R. G. Barbosa, Y. Li, L. -W. Hung, A. Matte, M. Cygler, Mo Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date :  25 Oct 02  (Deposition) - 28 Jan 03  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Trimer, P-Loop, Alpha/Beta, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. O'Toole, J. A. R. G. Barbosa, Y. Li, L. -W. Hung, A. Matte, M. Cygler
Crystal Structure Of A Trimeric Form Of Dephosphocoenzyme A Kinase From Escherichia Coli
Protein Sci. V. 12 327 2003
PubMed-ID: 12538896  |  Reference-DOI: 10.1110/PS.0227803
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEPHOSPHO-COA KINASE
    Chains: A, B, C
    EC Number: 2.7.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B DERIVATIVE
    Expression System Strain: DL41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COAE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DEPHOSPHOCOENZYME A KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO410Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:11 , GLY A:12 , SER A:13 , GLY A:14 , LYS A:15 , ARG A:144 , HOH A:528 , HOH A:604BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREILE B:11 , GLY B:12 , SER B:13 , GLY B:14 , LYS B:15 , ARG B:144 , HOH B:563 , HOH B:587BINDING SITE FOR RESIDUE SO4 B 502
03AC3SOFTWAREGLY C:12 , SER C:13 , GLY C:14 , LYS C:15 , ARG C:144 , HOH C:596BINDING SITE FOR RESIDUE SO4 C 503
04AC4SOFTWARESER A:119 , TYR A:121 , LYS A:122 , SER B:119 , TYR B:121 , LYS B:122 , HOH B:554 , SER C:119 , TYR C:121 , LYS C:122BINDING SITE FOR RESIDUE SO4 C 504
05AC5SOFTWAREARG A:126 , HIS A:192 , HOH A:576BINDING SITE FOR RESIDUE SO4 A 505
06AC6SOFTWAREARG B:126 , HIS B:192BINDING SITE FOR RESIDUE SO4 B 506
07AC7SOFTWAREARG C:126 , HIS C:192 , HOH C:653BINDING SITE FOR RESIDUE SO4 C 507
08AC8SOFTWAREHOH B:680 , GLN C:93 , THR C:96 , GLN C:97 , TRP C:110BINDING SITE FOR RESIDUE SO4 C 508
09AC9SOFTWAREALA A:157 , GLN B:93 , GLN B:97 , TRP B:110BINDING SITE FOR RESIDUE SO4 B 509
10BC1SOFTWAREGLN A:93 , THR A:96 , GLN A:97 , TRP A:110 , LYS A:123 , HOH C:650BINDING SITE FOR RESIDUE SO4 A 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N3B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala C:178 -Pro C:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N3B)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DPCKPS51219 Dephospho-CoA kinase (DPCK) domain profile.COAE_ECOLI4-200
 
 		  3A:4-200
B:4-200
C:4-200

(-) Exons   (0, 0)

(no "Exon" information available for 1N3B)

(-) 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:176
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:204
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQE 204
               SCOP domains d1n3ba_ A: Dephospho-CoA kinase                                                                                                                                                                              SCOP domains
               CATH domains -1n3bA00 A:2-204 P-loop containing nucleotide tri                            phosphate hydrolases                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhh..eeeehhhhhhhh....hhhhhh----------------------------.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---DPCK  PDB: A:4-200 UniProt: 4-200                                                                                                                                                                    ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n3b A   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHA----------------------------PEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQE 204
                            |       10        20        30        40        |-         -         -       |80        90       100       110       120       130       140 |     150       160       170       180       190       200    
                            |                                              49                           78                                                             142-MSE                                                          
                            1-MSE                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP 206
               SCOP domains d1n3bb_ B: Dephospho-CoA kinase                                                                                                                                                                                SCOP domains
               CATH domains -1n3bB00 B:2-206 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhh..eeeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: B:4-200 UniProt: 4-200                                                                                                                                                                    ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3b B   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANmIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP 206
                            |       10        20        30        40        50       |60        70        80        90       100       110       120       130       140 |     150       160       170       180       190       200      
                            1-MSE                                                   58-MSE                                                                             142-MSE                                                            


Chain C from PDB  Type:PROTEIN  Length:206
 aligned with COAE_ECOLI | P0A6I9 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
           COAE_ECOLI     1 MRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANMIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTMQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP 206
               SCOP domains d1n3bc_ C: Dephospho-CoA kinase                                                                                                                                                                                SCOP domains
               CATH domains -1n3bC00 C:2-206 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                          CATH domains
           Pfam domains (1) --CoaE-1n3bC01 C:3-181                                                                                                                                                               ------------------------- Pfam domains (1)
           Pfam domains (2) --CoaE-1n3bC02 C:3-181                                                                                                                                                               ------------------------- Pfam domains (2)
           Pfam domains (3) --CoaE-1n3bC03 C:3-181                                                                                                                                                               ------------------------- Pfam domains (3)
         Sec.struct. author ..eeeeee.....hhhhhhhhhhh...eeeehhhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhh.eeeeee.hhhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---DPCK  PDB: C:4-200 UniProt: 4-200                                                                                                                                                                    ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n3b C   1 mRYIVALTGGIGSGKSTVANAFADLGINVIDADIIARQVVEPGAPALHAIADHFGANmIAADGTLQRRALRERIFANPEEKNWLNALLHPLIQQETQHQIQQATSPYVLWVVPLLVENSLYKKANRVLVVDVSPETQLKRTmQRDDVTREHVEQILAAQATREARLAVADDVIDNNGAPDAIASDVARLHAHYLQLASQFVSQEKP 206
                            |       10        20        30        40        50       |60        70        80        90       100       110       120       130       140 |     150       160       170       180       190       200      
                            1-MSE                                                   58-MSE                                                                             142-MSE
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (COAE_ECOLI | P0A6I9)
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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        COAE_ECOLI | P0A6I9: 1t3h 1vhl 1vht 1viy

(-) Related Entries Specified in the PDB File

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