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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE SUGAR KINASE FROM CLOSTRIDIUM PERFRINGENS
 
Authors :  B. Syed Ibrahim, D. Kumaran, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  08 Dec 09  (Deposition) - 22 Dec 09  (Release) - 22 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nysgxrc, Psi-Ii, Sugar Kinase, Clostridium Perfringens, Protein Structure Initiative, Crystal Structure, 11209E, Modified Lysin, Structural Genomics, New York Sgx Research Center For Structural Genomics, Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Syed Ibrahim, D. Kumaran, S. K. Burley, S. Swaminathan
Crystal Structure Of A Putative Sugar Kinase From Clostridium Perfringens
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE SUGAR KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CPE1482
    Organism Scientific: CLOSTRIDIUM PERFRINGENS
    Organism Taxid: 1502

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 28)

Asymmetric/Biological Unit (2, 28)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2MSE26Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:166 , VAL A:168 , LYS A:187 , GLU A:192 , SER A:225 , HOH A:456BINDING SITE FOR RESIDUE BGC A 329
2AC2SOFTWAREASP B:166 , VAL B:168 , LYS B:187 , GLU B:192 , GLY B:256BINDING SITE FOR RESIDUE BGC B 329

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KZH)

(-) 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:316
 aligned with Q8XKB8_CLOPE | Q8XKB8 from UniProtKB/TrEMBL  Length:321

    Alignment length:316
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313      
         Q8XKB8_CLOPE     4 RKEPYLLVFGASVVDVFGFSKASYRPYNSTPGHVKISFGGVCRNIAENMARVGVNTNFMSILGNDEHGKSIVEHSKKIGYHMDDSMVIEGGSTPTYLAILDENGEMVSAIADMKSIGAMNTDFIDSKREIFENAEYTVLDSDNPEIMEYLLKNFKDKTNFILDPVSAEKASWVKHLIKDFHTIKPNRHEAEILAGFPITDTDDLIKASNYFLGLGIKKVFISLDADGIFYNDGVSCGKIKATEVDVKNVTGAGDSFVAGLGYGYMNKMPIEDIVKFAMTMSNITISHEETIHPDMALDTVLAKLEKTTWEEEKYDL 319
               SCOP domains d3kzha_ A: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeeee........eeeeeeeeeeehhhhhhhhhhhhh...eeee.ee..hhhhhhhhhhhhhhhee....ee.......eeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhh...hhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhhh..eeeee.hhh.eeee....eeeeee.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzh A   4 RKEPYLLVFGASVVDVFGFSKASYRPYNSTPGHVKISFGGVCRNIAENmARVGVNTNFmSILGNDEHGKSIVEHSKKIGYHmDDSmVIEGGSTPTYLAILDENGEmVSAIADmKSIGAmNTDFIDSKREIFENAEYTVLDSDNPEImEYLLKNFKDKTNFILDPVSAEKASWVKHLIKDFHTIKPNRHEAEILAGFPITDTDDLIKASNYFLGLGIKKVFISLDADGIFYNDGVSCGKIKATEVDVKNVTGAGDSFVAGLGYGYmNKmPIEDIVKFAmTmSNITISHEETIHPDmALDTVLAKLEKTTWEEEKYDL 319
                                    13        23        33        43        53        63        73        83 |   |  93       103     | 113  |    123       133       143      |153       163       173       183       193       203       213       223       233       243       253       263    |  273       283       293    |  303       313      
                                                                           52-MSE    62-MSE                 85-MSE                 109-MSE  |     |                         150-MSE                                                                                                               268-MSE      281-MSE          298-MSE                 
                                                                                                                89-MSE                    116-MSE |                                                                                                                                                  271-MSE     283-MSE                                
                                                                                                                                                122-MSE                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with Q8XKB8_CLOPE | Q8XKB8 from UniProtKB/TrEMBL  Length:321

    Alignment length:315
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314     
         Q8XKB8_CLOPE     5 KEPYLLVFGASVVDVFGFSKASYRPYNSTPGHVKISFGGVCRNIAENMARVGVNTNFMSILGNDEHGKSIVEHSKKIGYHMDDSMVIEGGSTPTYLAILDENGEMVSAIADMKSIGAMNTDFIDSKREIFENAEYTVLDSDNPEIMEYLLKNFKDKTNFILDPVSAEKASWVKHLIKDFHTIKPNRHEAEILAGFPITDTDDLIKASNYFLGLGIKKVFISLDADGIFYNDGVSCGKIKATEVDVKNVTGAGDSFVAGLGYGYMNKMPIEDIVKFAMTMSNITISHEETIHPDMALDTVLAKLEKTTWEEEKYDL 319
               SCOP domains d3kzhb_ B: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PfkB-3kzhB01 B:6-300                                                                                                                                                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) -PfkB-3kzhB02 B:6-300                                                                                                                                                                                                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author ....eeee...eeeeeeee.........eeeeeeeeeehhhhhhhhhhhhh...eeee.eee.hhhhhhhhhhhhhhh......eee......eeeeee.....eeeeeeehhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhh...hhhhh.ee..hhhhhhhhhh....hhhhhhhhhhhhhhh...eeeee.....eeee....eeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..-.....hhhhhhhhhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzh B   5 KEPYLLVFGASVVDVFGFSKASYRPYNSTPGHVKISFGGVCRNIAENmARVGVNTNFmSILGNDEHGKSIVEHSKKIGYHmDDSmVIEGGSTPTYLAILDENGEmVSAIADmKSIGAmNTDFIDSKREIFENAEYTVLDSDNPEImEYLLKNFKDKTNFILDPVSAEKASWVKHLIKDFHTIKPNRHEAEILAGFPITDTDDLIKASNYFLGLGIKKVFISLDADGIFYNDGVSCGKIKATEVDVKNVTGAGDSFVAGLGYGYmNKmPIEDIVKFAmTmSNITISHEE-IHPDmALDTVLAKLEKTTWEEEKYDL 319
                                    14        24        34        44       |54       |64        74        84|   |   94       104    |  114 |     124       134       144     | 154       164       174       184       194       204       214       224       234       244       254       264   |  |274      |284       294   |   304       314     
                                                                          52-MSE    62-MSE                 85-MSE                 109-MSE  |     |                         150-MSE                                                                                                               268-MSE      281-MSE    292 |   |                     
                                                                                                               89-MSE                    116-MSE |                                                                                                                                                  271-MSE     283-MSE    294   |                     
                                                                                                                                               122-MSE                                                                                                                                                                         298-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 3KZH)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8XKB8_CLOPE | Q8XKB8)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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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