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(-) Description

Title :  AATHIL COMPLEXED WITH AMPPCP
 
Authors :  K. M. Mcculloch, C. Kinsland, T. P. Begley, S. E. Ealick
Date :  18 Feb 08  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Barrel, Alpha-Beta Structure, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Mcculloch, C. Kinsland, T. P. Begley, S. E. Ealick
Structural Studies Of Thiamin Monophosphate Kinase In Complex With Substrates And Products.
Biochemistry V. 47 3810 2008
PubMed-ID: 18311927  |  Reference-DOI: 10.1021/BI800041H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMINE MONOPHOSPHATE KINASE
    Chains: A, B
    EC Number: 2.7.4.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: XF1
    Expression System Strain: B*R2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: THIL
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:42 , ASP A:43 , ASN B:119BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWAREASP A:27 , ASP A:71 , ASP A:207BINDING SITE FOR RESIDUE MG A 902
3AC3SOFTWAREASP A:43 , ASP A:71BINDING SITE FOR RESIDUE MG A 903
4AC4SOFTWAREASP B:27 , ASP B:71 , ASP B:207BINDING SITE FOR RESIDUE MG B 901
5AC5SOFTWAREASN A:119 , THR B:42 , ASP B:43BINDING SITE FOR RESIDUE MG B 902
6AC6SOFTWAREASP B:43 , ASP B:71BINDING SITE FOR RESIDUE MG B 903
7AC7SOFTWAREILE A:12 , ILE A:15 , ILE A:24 , GLY A:25 , ASP A:26 , ASP A:27 , ASP A:43 , ASP A:71 , ARG A:142 , SER A:209 , ILE B:84 , TYR B:101 , GLY B:117 , GLY B:118 , ASN B:119 , ILE B:120BINDING SITE FOR RESIDUE ACP B 900
8AC8SOFTWAREILE A:84 , TYR A:101 , GLY A:117 , GLY A:118 , ASN A:119 , ILE A:120 , GLU B:8 , ILE B:12 , ILE B:24 , GLY B:25 , ASP B:26 , ASP B:27 , ASP B:43 , ASP B:71 , ARG B:142 , SER B:209 , ASP B:210BINDING SITE FOR RESIDUE ACP A 900

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:34 -B:34

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C9S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C9S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C9S)

(-) Exons   (0, 0)

(no "Exon" information available for 3C9S)

(-) 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:304
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:304
                                1                                                                                                                                                                                                                                                                                                           
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
           THIL_AQUAE     - ----MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEP 300
               SCOP domains d3c9sa1 A:-3-137 Thiamine monophosphate kinase (ThiL) N-terminal domain                                                                      d3c9sa2 A:138-300 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                            SCOP domains
               CATH domains 3c9sA01 A:-3-140  [code=3.30.1330.10, no name defined]                                                                                          3c9sA02 A:141-300 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh.........eeeee..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeee.............eeee....hhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhh..eeee.hhhh..hhhhhhhhhhh..hhhhhhhhh....eeeeeehhhhh......eeeeeee...eeee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9s A  -3 GSFTMRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEP 300
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:302
                                 1                                                                                                                                                                                                                                                                                                        
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  
           THIL_AQUAE     - -----MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKK 297
               SCOP domains d3c9sb1 B:-4-137 Thiamine monophosphate kinase (ThiL) N-terminal domain                                                                       d3c9sb2 B:138-297 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                         SCOP domains
               CATH domains 3c9sB01 B:-4-140  [code=3.30.1330.10, no name defined]                                                                                           3c9sB02 B:141-297 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh........eeeee..eeeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeee.............eeee....hhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhh.eeee.hhhh..hhhhhhhhhhhh.hhhhhhhhh....eeeeeehhhhh......eeeeeee...eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9s B  -4 QGSFTMRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKK 297
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C9S)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (THIL_AQUAE | O67883)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0009030    thiamine-phosphate kinase activity    Catalysis of the reaction: ATP + thiamine phosphate = ADP + H(+) + thiamine diphosphate.
    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: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.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        THIL_AQUAE | O67883: 1vqv 3c9r 3c9t 3c9u

(-) Related Entries Specified in the PDB File

3c9r 3c9t 3c9u