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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROBABLE THIAMINE PYROPHOSPHOKINASE FROM STAPHYLOCOCCUS SAPROPHYTICUS SUBSP. SAPROPHYTICUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ID SYR86
 
Authors :  J. Seetharaman, S. Lew, D. Wang, H. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  31 Dec 09  (Deposition) - 09 Feb 10  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (3x),B (3x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Thiamin Diphosphate Biosynthetic Process, Atp Binding, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, S. Lew, D. Wang, H. Janjua, K. Cunningham, L. Owens, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Crystal Structure Of A Probable Thiamine Pyrophosphokinase From Staphylococcus Saprophyticus Subsp. Saprophyticus. Northeast Structural Genomics Consortium Target Id Syr86
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE THIAMINE PYROPHOSPHOKINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: SSP1549
    Organism Scientific: STAPHYLOCOCCUS SAPROPHYTICUS
    Organism Taxid: 342451
    Strain: SUBSP. SAPROPHYTICUS ATCC 15305 / DSM 20229

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A (3x)B (3x)
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NA3Ligand/IonSODIUM ION
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:93 , ASP A:94 , ASN A:124 , LYS A:126BINDING SITE FOR RESIDUE NA A 8001
2AC2SOFTWAREASN A:11 , GLY A:100 , HOH A:232 , ASN B:11 , HOH B:222BINDING SITE FOR RESIDUE NA A 8003
3AC3SOFTWAREGLN B:43 , ARG B:88 , TYR B:90BINDING SITE FOR RESIDUE NA B 8002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L8M)

(-) Exons   (0, 0)

(no "Exon" information available for 3L8M)

(-) 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:193
 aligned with Q49X04_STAS1 | Q49X04 from UniProtKB/TrEMBL  Length:211

    Alignment length:212
                                                                                                                                                                                                                                            211 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210| 
         Q49X04_STAS1     1 MKANLLCGNRNLPKHILVEHKHEHWIGIDRGTLILLESGITPQFAVGDFDSISDSERNFIQQQIEINPYNSEKDDTDLALGIDQAVKRGYRNIDVYGATGGRLDHFMGALQILEKPEYAKMNINIKLIDDTNEIQFIQKGQFNVTYSEQFPYISFIPVIYPTVISLKGFKYNLQNETLKLGSTLTISNELSQSCGNIEIIEGSVLMIRSKD-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........hhhhhh...eeeeehhhhhhhhhh.....eee......hhhhhhhhhhhh......---..hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee...eeeeee..eee..-----..eeeeee..-.eeee........ee.-------.......---...eeeee..eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8m A   1 mKANLLCGNRNLPKHILVEHKHEHWIGIDRGTLILLESGITPQFAVGDFDSISDSERNFIQQQIEINPYN---DDTDLALGIDQAVKRGYRNIDVYGATGGRLDHFmGALQILEKPEYAKmNINIKLIDDTNEIQFIQKGQFNV-----FPYISFIPVI-PTVISLKGFKYNLQNE-------LTISNEL---CGNIEIIEGSVLmIRSKDE 212
                            |       10        20        30        40        50        60        70   |    80        90       100      |110       120|      130       140   |   150        |-|      170     |   -   |   190   |   200     | 210  
                            |                                                                   70  74                              107-MSE       121-MSE                144   150      159 |            176     184   190 194         206-MSE  
                            1-MSE                                                                                                                                                         161                                                   


Chain B from PDB  Type:PROTEIN  Length:177
 aligned with Q49X04_STAS1 | Q49X04 from UniProtKB/TrEMBL  Length:211

    Alignment length:211
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210 
         Q49X04_STAS1     1 MKANLLCGNRNLPKHILVEHKHEHWIGIDRGTLILLESGITPQFAVGDFDSISDSERNFIQQQIEINPYNSEKDDTDLALGIDQAVKRGYRNIDVYGATGGRLDHFMGALQILEKPEYAKMNINIKLIDDTNEIQFIQKGQFNVTYSEQFPYISFIPVIYPTVISLKGFKYNLQNETLKLGSTLTISNELSQSCGNIEIIEGSVLMIRSKD 211
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------TPK_catalytic-3l8mB03 B:8-130                                                                                              ---------TPK_B1_binding-3l8m B01 B:140        -205                         ------ Pfam domains (1)
           Pfam domains (2) -------TPK_catalytic-3l8mB04 B:8-130                                                                                              ---------TPK_B1_binding-3l8m B02 B:140        -205                         ------ Pfam domains (2)
         Sec.struct. author .eeeee........hhhhhh....eeee.hhhhhhhhh.....eee...------.....-------------..hhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh..eeeee...eeeeee..eeeeee......eeeeee.-..eee....--------...hhhhh...---.eeeeeee---..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l8m B   1 mKANLLCGNRNLPKHILVEHKHEHWIGIDRGTLILLESGITPQFAVGDF------ERNFI-------------DDTDLALGIDQAVKRGYRNIDVYGATGGRLDHFmGALQILEKPEYAKmNINIKLIDDTNEIQFIQKGQFNVTYSEQFPYISFIPV-YPTVISLKG--------TLKLGSTLTIS---SQSCGNIE---GSVLmIRSKD 211
                            |       10        20        30        40        |-     |  60         -   |    80        90       100      |110       120|      130       140       150       160       | -      |180      |  -|      | - |   | 210 
                            1-MSE                                          49     56  60            74                              107-MSE       121-MSE                              158 |     168      177       187 191    198 202   |     
                                                                                                                                                                                         160                                           206-MSE
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3L8M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L8M)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: TPK_B1_binding] (4)
(-)
Clan: no clan defined [family: TPK_catalytic] (4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q49X04_STAS1 | Q49X04)
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:0030975    thiamine binding    Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0004788    thiamine diphosphokinase activity    Catalysis of the reaction: ATP + thiamine = AMP + thiamine diphosphate.
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: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.
    GO:0006772    thiamine metabolic process    The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

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