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(-) Description

Title :  CRYSTAL STRUCTURE OF THIAMINE MONOPHOSPHATE KINASE (THIL) FROM AQUIFEX AEOLICUS
 
Authors :  S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Jan 05  (Deposition) - 11 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thil, Kinase, Dimer, Phosphate, New York Sgx Research Center For Structural Genomics, Nysgxrc, Protein Structure Initiative, Psi, T1881, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. Swaminathan
Crystal Structure Of Thiamine Monophosphate Kinase (Thil) From Aquifex Aeolicus
To Be Published
PubMed: search
(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 Taxid: 562
    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, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:184 , ASN A:238 , GLU A:239 , SER B:95BINDING SITE FOR RESIDUE PO4 A 1001
2AC2SOFTWAREILE A:56 , GLU A:58 , ALA A:59 , TRP A:62 , ARG A:106 , ARG A:187 , TRP B:273BINDING SITE FOR RESIDUE PO4 A 1002
3AC3SOFTWARESER A:95 , SER B:237 , ASN B:238 , GLU B:239BINDING SITE FOR RESIDUE PO4 B 1003
4AC4SOFTWARETRP A:273 , ILE B:56 , GLU B:58 , ALA B:59 , TRP B:62 , ARG B:106 , ARG B:187BINDING SITE FOR RESIDUE PO4 B 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VQV)

(-) Exons   (0, 0)

(no "Exon" information available for 1VQV)

(-) 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:292
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
           THIL_AQUAE     1 MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEP 300
               SCOP domains d1vqva   1 A:1-137 Thiam ine mo   nophosphate kinase (ThiL) N-terminal domain                                                            d1vqva2 A:138-300 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                            SCOP domains
               CATH domains -1vqvA   01 A:2-140  [co de=3.3   0.1330.10, no name defined]                                                                               1vqvA02 A:141-300 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......---.hhhhhhhhhh....-......---..eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeee..eee....eeeeeeeeee.............eeee....hhhhhhhhhhh......hhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhh.eeee.hhhh..hhhhhhhhhhhh.hhhhhhhh.......eeee...........eeeeeee..-.eee..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vqv A   1 mRLKEL---GLIDLIKKTLESKVI-DDTAPV---SKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLmEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASmDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKmYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDmTEIGRVEEG-GVFVDGKKVEP 300
                            |    |  10        20   | |  30|   |   40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     | 210       220       230       240 |     250       260       270       280       290       300
                            |    6  10            24 |   31  35                                                                                                                                   169-MSE                              206-MSE                             242-MSE                              279-MSE  288 |          
                            1-MSE                   26                                                                                                                                                                                                                                                                     290          


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with THIL_AQUAE | O67883 from UniProtKB/Swiss-Prot  Length:306

    Alignment length:300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
           THIL_AQUAE     1 MRLKELGEFGLIDLIKKTLESKVIGDDTAPVEYCSKKLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLMEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASMDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKMYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDMTEIGRVEEGEGVFVDGKKVEP 300
               SCOP domains d1vqvb1 B:1-137 Thiamine  monoph    osphate kinase (ThiL) N-terminal domain                                                              d1vqvb2 B:138-300 Thiamine monophosphate kinase (ThiL) C-terminal domain                                                                                            SCOP domains
               CATH domains -1vqvB01 B:2-140  [code= 3.30.13    30.10, no name defined]                                                                                 1vqvB02 B:141-300 Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....-.......----.eeeeeeeee.........hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeee..eee....eeeeeeeeee.............eeee....hhhhhhhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhh.eeee...hhhhhhhhhhhhh..eeee.hhhh..hhhhhhhhhhh..hhhhhhhh......eeeeehhhhh......eeeeeee....eee..ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vqv B   1 mRLKELGEFGLIDLIKKTLESKVI-DDTAPVE----KLLLTTDVLNEGVHFLRSYIPEAVGWKAISVNVSDVIANGGLPKWALISLNLPEDLEVSYVERFYIGVKRACEFYKCEVVGGNISKSEKIGISVFLVGETERFVGRDGARLGDSVFVSGTLGDSRAGLELLLmEKEEYEPFELALIQRHLRPTARIDYVKHIQKYANASmDISDGLVADANHLAQRSGVKIEILSEKLPLSNELKmYCEKYGKNPIEYALFGGEDYQLLFTHPKERWNPFLDmTEIGRVEEGEGVFVDGKKVEP 300
                            |       10        20   | |  30 |    | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     | 210       220       230       240 |     250       260       270       280       290       300
                            1-MSE                 24 |    32   37                                                                                                                                 169-MSE                              206-MSE                             242-MSE                              279-MSE                 
                                                    26
   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 1VQV)

(-) 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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        THIL_AQUAE | O67883: 3c9r 3c9s 3c9t 3c9u

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