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(-) Description

Title :  CRYSTAL STRUCTURE OF FRUCTOKINASE WITH BOUND ATP FROM XYLELLA FASTIDIOSA
 
Authors :  L. Satyanarayana, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  27 Jan 10  (Deposition) - 09 Mar 10  (Release) - 09 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Kinase, Fructokinase, Atp, Potassium Ion, 11206H, Psi2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Satyanarayana, S. K. Burley, S. Swaminathan
Crystal Structure Of Fructokinase With Bound Atp From Xylella Fastidiosa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - FRUCTOKINASE
    Chains: A, B
    EC Number: 2.7.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSGX3
    Expression System Strain: BL21 (DE3) CODON + RIL
    Expression System Taxid: 469008
    Expression System Vector: BC-PSGX3 (BC)
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 12-338
    Gene: 1143885, PD_1163
    Organism Scientific: XYLELLA FASTIDIOSA
    Organism Taxid: 183190
    Strain: TEMECULA1 / ATCC 700964

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric Unit (4, 22)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K1Ligand/IonPOTASSIUM ION
3MSE19Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MSE9Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 21)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MSE19Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:264 , ASN B:266 , ALA B:314 , ARG B:317 , GLY B:319 , ALA B:323BINDING SITE FOR RESIDUE K B 901
2AC2SOFTWAREALA B:46 , ASN B:49 , ASN B:176 , ARG B:178 , ASP B:270 , ATP B:900BINDING SITE FOR RESIDUE PO4 B 501
3AC3SOFTWAREARG B:178 , LYS B:203 , THR B:238 , ASP B:239 , ALA B:240 , VAL B:244 , THR B:257 , PHE B:258 , VAL B:262 , ALA B:268 , GLY B:269 , ALA B:308 , HOH B:394 , HOH B:436 , PO4 B:501BINDING SITE FOR RESIDUE ATP B 900

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:117 -Pro A:118
2Pro A:118 -Pro A:119
3Mse A:324 -Pro A:325
4Arg B:117 -Pro B:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LKI)

(-) 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:313
 aligned with Q87CC0_XYLFT | Q87CC0 from UniProtKB/TrEMBL  Length:338

    Alignment length:329
                                                                                                                                                                                                                                                                                                                                                                 338 
                                    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       | 
         Q87CC0_XYLFT    11 KKKTILCFGEALIDMLAQPLVKKGMPRAFLQCAGGAPANVAVAVARLGGAVQFVGMLGSDMFGDFLFDSFAEAGVVTDGIVRTSTAKTALAFVALDAHGERSFSFYRPPAADLLFRVEHFQDASFSDALIFHACSNSMTDADIAEVTFEGMRRAQAAGAIVSFDLNFRPMLWPNGENPASRLWKGLSLADVVKLSSEELDYLANTLAADANAVIQQLWQGRAQLLLVTDAAGPVHWYTRTAGGEVPTFRVQVQDSNAAGDAFVGGMLYTFAQQFDDAAALIDFCHDPESIVSTLRFAAAVGALAVTRQGAFTAMPMLSEVLSLIQEQS-   -
               SCOP domains d3lkia_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee...........eeeeeehhhhhhhhhhhhhh..eeee.eee.hhhhhhhhhhhhhhh......eee......eeeee.--....eeeee...hhhhhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhh.....hhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhhhhhhhh....eeeee.....eeeee...eeee...----------hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lki A  -1 LKKTILCFGEALIDmLAQPLVKKGmPRAFLQCAGGAPANVAVAVARLGGAVQFVGmLGSDmFGDFLFDSFAEAGVVTDGIVRTSTAKTALAFVAL--HGERSFSFYRPPAADLLFRVEHFQDASFSDALIFHACSNSmTDADIAEVTFEGmRRAQAAGAIVSFDLNFRPmLWPNGENPASRLWKGLSLADVVKLSSEELDYLANTLAADANAVIQQLWQGRAQLLLVTDAAGPVHWYTRTAGGEVPTF----------GDAFVGGmLYTFAQQFDDAAALIDFCHDPESIVSTLRFAAAVGALAV----AFTAmPmLSEVLSLIQEQSE 339
                            ||      20    |   30    |   40        50        60     |  70|       80        90       100    |  110       120       130       140       150       160|      170       180       190       200       210       220       230       240       250       | -       270     | 280       290       300       310    |  320   | | 330         
                            ||           25-MSE    35-MSE                         66-MSE|                               105  |                                     148-MSE      161-MSE            180-MSE                                                                       258        269      |                                    315  320   | |             
                           -1|                                                         71-MSE                              108                                                                                                                                                                     276-MSE                                         324-MSE           
                            12                                                                                                                                                                                                                                                                                                                       326-MSE         


Chain B from PDB  Type:PROTEIN  Length:322
 aligned with Q87CC0_XYLFT | Q87CC0 from UniProtKB/TrEMBL  Length:338

    Alignment length:329
                                                                                                                                                                                                                                                                                                                                                                 338 
                                    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       | 
         Q87CC0_XYLFT    11 KKKTILCFGEALIDMLAQPLVKKGMPRAFLQCAGGAPANVAVAVARLGGAVQFVGMLGSDMFGDFLFDSFAEAGVVTDGIVRTSTAKTALAFVALDAHGERSFSFYRPPAADLLFRVEHFQDASFSDALIFHACSNSMTDADIAEVTFEGMRRAQAAGAIVSFDLNFRPMLWPNGENPASRLWKGLSLADVVKLSSEELDYLANTLAADANAVIQQLWQGRAQLLLVTDAAGPVHWYTRTAGGEVPTFRVQVQDSNAAGDAFVGGMLYTFAQQFDDAAALIDFCHDPESIVSTLRFAAAVGALAVTRQGAFTAMPMLSEVLSLIQEQS-   -
               SCOP domains d3lkib_ B: automated      matches                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PfkB-3lkiB01 B:12-3     27                                                                                                                                                                                                                                                                                                  ------------ Pfam domains (1)
           Pfam domains (2) -PfkB-3lkiB02 B:12-3     27                                                                                                                                                                                                                                                                                                  ------------ Pfam domains (2)
         Sec.struct. author ...eeeee...eeeeee...-----...eeeeeehhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhh.....eeee......eeeeee.--..eeeeee...hhhhhhhhhhhhhhhhhheeeeeee.hhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhh.....hhhhhhhhhhh..eeeeehhhhhhhhhhh..hhhhhhhhhhh....eeeee.....eeee....eeee...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lki B  -1 LKKTILCFGEALIDmLAQPL-----PRAFLQCAGGAPANVAVAVARLGGAVQFVGmLGSDmFGDFLFDSFAEAGVVTDGIVRTSTAKTALAFVALD--GERSFSFYRPPAADLLFRVEHFQDASFSDALIFHACSNSmTDADIAEVTFEGmRRAQAAGAIVSFDLNFRPmLWPNGENPASRLWKGLSLADVVKLSSEELDYLANTLAADANAVIQQLWQGRAQLLLVTDAAGPVHWYTRTAGGEVPTFRVQVQDSNAAGDAFVGGmLYTFAQQFDDAAALIDFCHDPESIVSTLRFAAAVGALAVTRQGAFTAmPmLSEVLSLIQEQSE 339
                            ||      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         
                           -1|           25-MSE0    36                            66-MSE|                                106  |                                    148-MSE      161-MSE            180-MSE                                                                                         276-MSE                                         324-MSE           
                            12                                                         71-MSE                               109                                                                                                                                                                                                                      326-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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q87CC0_XYLFT | Q87CC0)
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: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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol 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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q87CC0_XYLFT | Q87CC0: 3ljs

(-) Related Entries Specified in the PDB File

3ljs CRYSTAL STRUCTURE OF FRUCTOKINASE FROM XYLELLA FASTIDIOSA RELATED ID: NYSGXRC-11206H RELATED DB: TARGETDB