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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROPIONATE KINASE FROM FRANCISELLA TULARENSIS SUBSP. TULARENSIS SCHU S4
 
Authors :  J. S. Brunzelle, T. Skarina, S. Sharma, Y. Wang, A. Savchenko, W. F. Ande Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  31 Oct 09  (Deposition) - 19 Jan 10  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Propionate Kinase, Csgid, Idp01739, Atp-Binding, Kinase, Nucleotide- Binding, Transferase, Structural Genomics, National Institute Of Allergy And Infectious Diseases, National Institutes Of Health, Department Of Health And Human Services, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Brunzelle, S. S. Sharma, T. Skarina, Y. Wang, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of A Propionate Kinase From Francisella Tularensis Subsp. Tularensis Schu S4
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROPIONATE KINASE
    Chains: A, B
    EC Number: 2.7.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21-CODONPLUS(DE3)-RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTT1753, FTT_1753, TDCD
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 22)

Asymmetric/Biological Unit (1, 22)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3KHY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KHY)

(-) 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:384
 aligned with Q5NE95_FRATT | Q5NE95 from UniProtKB/TrEMBL  Length:384

    Alignment length:384
                                    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       310       320       330       340       350       360       370       380    
         Q5NE95_FRATT     1 MSEILVLNCGSSSVKFALINPHTSQSLVTGLAENIATKNCKVVFKAEHKIVKYLENGSYKDVFEMLKDFLVENKHLEKIVAIGHRVVHGGQYFSKSVLINADSLEKIKACIALAPLHNPAHIEGIRFCQQIFPELPQVAVFDTAFHQTMPSYIAEYAIPYELTHKHNIRKYGAHGTSHKYVSEQAAKILTQQKANVIVAHLGNGCSITAVVDGKSIDTSMGLTPLDGLVMGTRSGCIDPSIFAYISDNLGWSVTEITNMLNKQSGLLGICGHNDMREVSQLAAKGDSLAKLAIEIFSHRVAKFVASYMIYFNKLDALVFTGGIGENAANIRKNIISKLANLGFMIDHQKNSNSETFINSKNSHNIMVIATNEELMIAQETQNLI 384
               SCOP domains d3khya1 A:1-190 automated matches                                                                                                                                                             d3khya2 A:191-384 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3khyA02 A:191-384  [code=3.30.420.40, no name defined]                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeeee.......eeeee...eeeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh......eeeeee...eeeeeee..eeeee.....................hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhh............eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3khy A   1 mSEILVLNCGSSSVKFALINPHTSQSLVTGLAENIATKNCKVVFKAEHKIVKYLENGSYKDVFEmLKDFLVENKHLEKIVAIGHRVVHGGQYFSKSVLINADSLEKIKACIALAPLHNPAHIEGIRFCQQIFPELPQVAVFDTAFHQTmPSYIAEYAIPYELTHKHNIRKYGAHGTSHKYVSEQAAKILTQQKANVIVAHLGNGCSITAVVDGKSIDTSmGLTPLDGLVmGTRSGCIDPSIFAYISDNLGWSVTEITNmLNKQSGLLGICGHNDmREVSQLAAKGDSLAKLAIEIFSHRVAKFVASYmIYFNKLDALVFTGGIGENAANIRKNIISKLANLGFmIDHQKNSNSETFINSKNSHNImVIATNEELmIAQETQNLI 384
                            |       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       310       320       330       340   |   350       360     | 370    |  380    
                            |                                                              65-MSE                                                                             149-MSE                                                                220-MSE   230-MSE                      259-MSE         275-MSE                          308-MSE                             344-MSE               366-MSE  375-MSE     
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:384
 aligned with Q5NE95_FRATT | Q5NE95 from UniProtKB/TrEMBL  Length:384

    Alignment length:384
                                    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       310       320       330       340       350       360       370       380    
         Q5NE95_FRATT     1 MSEILVLNCGSSSVKFALINPHTSQSLVTGLAENIATKNCKVVFKAEHKIVKYLENGSYKDVFEMLKDFLVENKHLEKIVAIGHRVVHGGQYFSKSVLINADSLEKIKACIALAPLHNPAHIEGIRFCQQIFPELPQVAVFDTAFHQTMPSYIAEYAIPYELTHKHNIRKYGAHGTSHKYVSEQAAKILTQQKANVIVAHLGNGCSITAVVDGKSIDTSMGLTPLDGLVMGTRSGCIDPSIFAYISDNLGWSVTEITNMLNKQSGLLGICGHNDMREVSQLAAKGDSLAKLAIEIFSHRVAKFVASYMIYFNKLDALVFTGGIGENAANIRKNIISKLANLGFMIDHQKNSNSETFINSKNSHNIMVIATNEELMIAQETQNLI 384
               SCOP domains d3khyb1 B:1-190 automated matches                                                                                                                                                             d3khyb2 B:191-384 automated matches                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3khyB02 B:191-384  [code=3.30.420.40, no name defined]                                                                                                                                             CATH domains
           Pfam domains (1) --Acetate_kinase-3khyB01 B:3-378                                                                                                                                                                                                                                                                                                                                                          ------ Pfam domains (1)
           Pfam domains (2) --Acetate_kinase-3khyB02 B:3-378                                                                                                                                                                                                                                                                                                                                                          ------ Pfam domains (2)
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeeee.......eeeee...eeeee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh......eeeeee...eeeeeee..eeeee.....................hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhh............eee...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3khy B   1 mSEILVLNCGSSSVKFALINPHTSQSLVTGLAENIATKNCKVVFKAEHKIVKYLENGSYKDVFEmLKDFLVENKHLEKIVAIGHRVVHGGQYFSKSVLINADSLEKIKACIALAPLHNPAHIEGIRFCQQIFPELPQVAVFDTAFHQTmPSYIAEYAIPYELTHKHNIRKYGAHGTSHKYVSEQAAKILTQQKANVIVAHLGNGCSITAVVDGKSIDTSmGLTPLDGLVmGTRSGCIDPSIFAYISDNLGWSVTEITNmLNKQSGLLGICGHNDmREVSQLAAKGDSLAKLAIEIFSHRVAKFVASYmIYFNKLDALVFTGGIGENAANIRKNIISKLANLGFmIDHQKNSNSETFINSKNSHNImVIATNEELmIAQETQNLI 384
                            |       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       310       320       330       340   |   350       360     | 370    |  380    
                            1-MSE                                                          65-MSE                                                                             149-MSE                                                                220-MSE   230-MSE                      259-MSE         275-MSE                          308-MSE                             344-MSE               366-MSE  375-MSE
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5NE95_FRATT | Q5NE95)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008776    acetate kinase activity    Catalysis of the reaction: ATP + acetate = ADP + acetyl phosphate.
    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:0016774    phosphotransferase activity, carboxyl group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor).
    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:0006085    acetyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006082    organic acid metabolic process    The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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