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(-) Description

Title :  CRYSTAL STRUCTURE OF AN UNCHARACTERIZED SUGAR KINASE PH1459 FROM PYROCOCCUS HORIKOSHII
 
Authors :  G. Kumar, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  15 Oct 08  (Deposition) - 18 Nov 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carbohydrate Kinase, Pfkb Family, Psi-Ii, 11207G, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Kumar, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of An Uncharacterized Sugar Kinase Ph1459 From Pyrococcus Horikoshii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED SUGAR KINASE PH1459
    Chains: A, B
    EC Number: 2.7.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21 (DE3) CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH1459, PHCC008
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3EWM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:138 -Pro A:139
2Asn B:138 -Pro B:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_1PS00583 pfkB family of carbohydrate kinases signature 1.Y1459_PYRHO37-61
 		  2A:33-57
B:33-57
2PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.Y1459_PYRHO245-258
 		  2A:241-254
B:244-254

(-) Exons   (0, 0)

(no "Exon" information available for 3EWM)

(-) 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:304
 aligned with Y1459_PYRHO | O59128 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:304
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305    
          Y1459_PYRHO     6 GMIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNMTLNDINWDIVEEAKIVNFGSVILARNPSRETVMKVIKKIKGSSLIAFDVNLRLDLWRGQEEEMIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSMLTAITLGPKGCRLIKNETVVDVPSYNVNPLDTTGAGDAFMAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 309
               SCOP domains d3ewma_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee..........eeeeeeehhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeee......eeee...hhhhh.hhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhhhhhhhh.eeeeehhhhhhhhh.........eeeee....eeeeee..eeeeee..........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PFKB_KINASES_1           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2--------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ewm A   2 SLIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNmTLNDINWDIVEEAKIVNFGSVILARNPSRETVmKVIKKIKGSSLIAFDVNLRLDLWRGQEEEmIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSmLTAITLGPKGCRLIKNETVVDVPSYNVNPLDTTGAGDAFmAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLA 305
                                    11        21        31        41        51        61        71        81        91       101       111|      121       131       141   |   151       161       171   |   181       191       201       211       221       231       241       251       261       271       281       291       301    
                                                                                                                                        112-MSE                          145-MSE                       175-MSE                            210-MSE                                 250-MSE                                                   


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Y1459_PYRHO | O59128 from UniProtKB/Swiss-Prot  Length:310

    Alignment length:304
                                    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    
          Y1459_PYRHO     7 MIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNMTLNDINWDIVEEAKIVNFGSVILARNPSRETVMKVIKKIKGSSLIAFDVNLRLDLWRGQEEEMIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSMLTAITLGPKGCRLIKNETVVDVPSYNVNPLDTTGAGDAFMAALLVGILKLKGLDLLKLGKFANLVAALSTQKRGAWSTPRKDELLKYKEAREVLAP 310
               SCOP domains d3ewmb_ B: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeeee..........eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee.....eeeeee......eeee...hhhhh.hhhhhhhhhhhhh.eeeee.hhhhh.hhhhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhhhhhhhh.eeeeehhhhhhhhh.........eeeee.hhh.eeeee..eeeee..---------hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh----.....hhhhh..hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------PFKB_KINASES_1           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ewm B   3 LIASIGELLIDLISVEEGDLKDVRLFEKHPGGAPANVAVGVSRLGVKSSLISKVGNDPFGEYLIEELSKENVDTRGIVKDEKKHTGIVFVQLKGASPSFLLYDDVAYFNmTLNDINWDIVEEAKIVNFGSVILARNPSRETVmKVIKKIKGSSLIAFDVNLRLDLWRGQEEEmIKVLEESIKLADIVKASEEEVLYLENQGVEVKGSmLTAITLGPKGCRLIKNETVVDVPS---------GAGDAFmAALLVGILKLKGLDLLKLGKFANLVAALST----AWSTPRKDELLKYKEAREVLAE 306
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142  |    152       162       172  |    182       192       202       212       222       232 |       - |     252       262       272       | -  |    292       302    
                                                                                                                                       112-MSE                          145-MSE                       175-MSE                            210-MSE                 234       244     |                           280  285                     
                                                                                                                                                                                                                                                                                 250-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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y1459_PYRHO | O59128)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0004747    ribokinase activity    Catalysis of the reaction: ATP + D-ribose = ADP + D-ribose 5-phosphate.
    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:0006014    D-ribose metabolic process    The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
    GO:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    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/Swiss-Prot
        Y1459_PYRHO | O59128: 3gbu 3ih0

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