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(-) Description

Title :  CRYSTAL STRUCTURE OF THIAMINE-MONOPHOSPHATE KINASE (MFLA_0573) FROM METHYLOBACILLUS FLAGELLATUS KT AT 1.91 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  29 Mar 10  (Deposition) - 19 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Thiamine-Monophosphate Kinase (Mfla_0573) From Methylobacillus Flagellatus Kt At 1. 91 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIAMINE-MONOPHOSPHATE KINASE
    Chains: A
    EC Number: 2.7.4.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MFLA_0573
    Organism Scientific: METHYLOBACILLUS FLAGELLATUS
    Organism Taxid: 265072
    Strain: KT / ATCC 51484 / DSM 6875

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2MSE7Mod. Amino AcidSELENOMETHIONINE
3NA2Ligand/IonSODIUM ION
4PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (5, 30)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2MSE14Mod. Amino AcidSELENOMETHIONINE
3NA-1Ligand/IonSODIUM ION
4PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE4Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARE1PE A:328 , HOH A:357BINDING SITE FOR RESIDUE NA A 319
02AC2SOFTWAREPG4 A:327 , HOH A:400BINDING SITE FOR RESIDUE NA A 320
03AC3SOFTWAREILE A:167 , LEU A:178 , GLY A:182 , HIS A:186 , PGE A:326BINDING SITE FOR RESIDUE PEG A 321
04AC4SOFTWAREGLN A:250 , LEU A:307BINDING SITE FOR RESIDUE PEG A 322
05AC5SOFTWAREARG A:80 , ASP A:111 , ALA A:113BINDING SITE FOR RESIDUE PEG A 323
06AC6SOFTWAREALA A:19 , VAL A:23BINDING SITE FOR RESIDUE PEG A 324
07AC7SOFTWARELYS A:183BINDING SITE FOR RESIDUE PGE A 325
08AC8SOFTWAREASP A:56 , LEU A:59 , GLN A:187 , SER A:241 , GLN A:245 , PEG A:321BINDING SITE FOR RESIDUE PGE A 326
09AC9SOFTWAREARG A:10 , PHE A:12 , ILE A:55 , LEU A:59 , LYS A:63 , HIS A:186 , ASP A:258 , NA A:320 , HOH A:400BINDING SITE FOR RESIDUE PG4 A 327
10BC1SOFTWARELYS A:232 , ALA A:233 , ILE A:234 , PRO A:235 , GLU A:238 , SER A:241 , ASP A:284 , ALA A:286 , NA A:319BINDING SITE FOR RESIDUE 1PE A 328

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MCQ)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MCQ)

(-) Sequences/Alignments

Asymmetric 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:302
 aligned with Q1H3U4_METFK | Q1H3U4 from UniProtKB/TrEMBL  Length:318

    Alignment length:302
                                    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       306  
         Q1H3U4_METFK     7 LIQRYFRRAHPSAVLGVGDDAALIQPSPGMELAVSADMLVANTHFYPNIDPWLIGWKSLAVNISDMAAMGAQPRWATLTIALPEADEDWISKFAAGFFACAAQFDIALIGGDTTRGPLTISVQIMGETPPGASLLRSTARADDDIWVSGPLGDAALALAAIQGRYPLSDTELAACGKALHQPQPRVVLGQALRGLAHSALDISDGLLADLGHILEHSQVGAEVWLKAIPKSEVVSAHSQEVAIQKMILSGGDDYELCFTASTQHRQQIADIGRQLSLDMAVIGRITDTQQLVIHGLDDAPLT 308
               SCOP domains d3mcqa1 A:7-135 automated matches                                                                                                d3mcqa2 A:136-308 automated matches                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........ee......hhhhhh.......eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeeee..............eeeee....hhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhh...eeeeee...hhhhhhhhhhhhhh.eeeee.hhh..hhhhhhh..hhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh....eeeeeee....eeee.....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcq A   7 LIQRYFRRAHPSAVLGVGDDAALIQPSPGmELAVSADmLVANTHFYPNIDPWLIGWKSLAVNISDmAAmGAQPRWATLTIALPEADEDWISKFAAGFFACAAQFDIALIGGDTTRGPLTISVQImGETPPGASLLRSTARADDDIWVSGPLGDAALALAAIQGRYPLSDTELAACGKALHQPQPRVVLGQALRGLAHSALDISDGLLADLGHILEHSQVGAEVWLKAIPKSEVVSAHSQEVAIQKmILSGGDDYELCFTASTQHRQQIADIGRQLSLDmAVIGRITDTQQLVIHGLDDAPLT 308
                                    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       306  
                                                        36-MSE  44-MSE                      72-MSE                                                    131-MSE                                                                                                                  252-MSE                          285-MSE                   
                                                                                               75-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MCQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1H3U4_METFK | Q1H3U4)
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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