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(-) Description

Title :  AATHIL COMPLEXED WITH AMPPCP AND TMP
 
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 :  2.60
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  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2MG10Ligand/IonMAGNESIUM ION
3TPS2Ligand/IonTHIAMIN PHOSPHATE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:210BINDING SITE FOR RESIDUE MG A 309
02AC2SOFTWAREASP A:43 , ASP A:71BINDING SITE FOR RESIDUE MG A 310
03AC3SOFTWAREASP A:43 , ASN B:119BINDING SITE FOR RESIDUE MG B 311
04AC4SOFTWAREASP A:210 , ASP A:215 , HIS A:218BINDING SITE FOR RESIDUE MG A 312
05AC5SOFTWAREASP A:27 , ASP A:71 , ASP A:207BINDING SITE FOR RESIDUE MG A 313
06AC6SOFTWAREASN A:119 , ASP B:43BINDING SITE FOR RESIDUE MG A 314
07AC7SOFTWAREASP B:210BINDING SITE FOR RESIDUE MG B 310
08AC8SOFTWAREASP B:27 , ASP B:71 , ASP B:207BINDING SITE FOR RESIDUE MG B 312
09AC9SOFTWAREASP B:43 , ASP B:71BINDING SITE FOR RESIDUE MG B 313
10BC1SOFTWAREASP B:210 , ASP B:215 , HIS B:218BINDING SITE FOR RESIDUE MG B 314
11BC2SOFTWAREILE A:12 , ILE A:24 , GLY A:25 , ASP A:26 , ASP A:27 , ASP A:43 , ASP A:71 , ARG A:142 , SER A:209 , HIS A:218 , HOH A:320 , HOH A:322 , ILE B:84 , TYR B:101 , GLY B:117 , GLY B:118 , ASN B:119 , ILE B:120BINDING SITE FOR RESIDUE ACP B 307
12BC3SOFTWAREGLY A:48 , HIS A:50 , LEU A:164 , ASP A:210 , GLU A:260 , TRP A:303 , HIS A:305BINDING SITE FOR RESIDUE TPS A 308
13BC4SOFTWAREILE A:84 , LEU A:86 , TYR A:101 , GLY A:117 , GLY A:118 , ASN A:119 , ILE A:120 , HOH A:318 , HOH A:321 , 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 , HIS B:218 , HOH B:318BINDING SITE FOR RESIDUE ACP A 307
14BC5SOFTWAREGLY B:48 , HIS B:50 , LEU B:164 , HIS B:185 , ASP B:210 , GLU B:260 , TRP B:303 , HIS B:305BINDING SITE FOR RESIDUE TPS B 308

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu B:299 -Pro B:300

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C9T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C9T)

(-) Exons   (0, 0)

(no "Exon" information available for 3C9T)

(-) 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:307
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:307
                             1                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       
           THIL_AQUAE     - -MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEPKGWKHF 306
               SCOP domains d3c9ta1 A:0-137 Thiamine monophosphate kinase (ThiL) N-terminal domain                                                                    d3c9ta2 A:138-306 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                                  SCOP domains
               CATH domains 3c9tA01 A:0-140  [code=3.30.1330.10, no name defined]                                                                                        3c9tA02 A:141-306 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh........eeee....eeeeeeeeee.........hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeeeeeee.............eeeee...hhhhhhhhhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh.eeee.hhhh..hhhhhhhhhhhh.hhhhhhhhh.....eeeeehhhhh.....eeeeeeee....eee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c9t A   0 TMRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEPKGWKHF 306
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:309
                               1                                                                                                                                                                                                                                                                                                                 
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297         
           THIL_AQUAE     - ---MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEPKGWKHF 306
               SCOP domains d3c9tb1 B:-2-137 Thiamine monophosphate kinase (ThiL) N-terminal domain                                                                     d3c9tb2 B:138-306 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                                  SCOP domains
               CATH domains 3c9tB01 B:-2-140  [code=3.30.1330.10, no name defined]                                                                                         3c9tB02 B:141-306 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
                 3c9t B  -2 SFTMRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEPKGWKHF 306
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
   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 3C9T)

(-) 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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  3c9t
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  2.7.4.16
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 Related Entries

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

UniProtKB/Swiss-Prot
        THIL_AQUAE | O67883: 1vqv 3c9r 3c9s 3c9u

(-) Related Entries Specified in the PDB File

3c9r 3c9s 3c9u