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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLULOKINASE FROM CHROMOBACTERIUM VIOLACEUM
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  08 Dec 09  (Deposition) - 09 Mar 10  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Xylulokinase, Chromobacterium Violaceum, Adp, Sgx, Carbohydrate Kinase, 11200B, Kinase, Transferase, Structural Genomics, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, S. K. Burley, S. Swaminathan
Crystal Structure Of Xylulokinase From Chromobacterium Violaceum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - XYLULOKINASE
    Chains: A
    EC Number: 2.7.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3) CODEN+RIL STRATAGENE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: XYLB, CV_1862
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Strain: ATCC 12472

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:262 , THR A:263 , GLY A:305 , ASN A:306 , GLN A:309 , PHE A:327 , GLY A:409 , GLY A:410 , ARG A:412 , HOH A:564BINDING SITE FOR RESIDUE ADP A 1760

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:354 -A:392

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Cys A:354 -Pro A:355

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KZB)

(-) 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    
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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:498
 aligned with Q7NWW7_CHRVO | Q7NWW7 from UniProtKB/TrEMBL  Length:501

    Alignment length:500
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499
         Q7NWW7_CHRVO     - -MAFYIATFDIGTTEVKAALADRDGGLHFQRSIALETYGDGNGPVEQDAGDWYDAVQRIASSWWQSGVDARRVSAIVLSGQMQNFLPLDQDHEPLHRAVLYSDKRPLKEAEEINARHGADNLWSALENPMTAASILPKLVFWRASFPQAFGRLRHVVLGAKDYVVLRLTGRHATDRTNASTTGLYRPKDDAWHVELLADYGFSLDLMPRLLEPGEQVGGVSALAARQTGFVSGTPVLCGLGDAGAATLGVGVLDDEDAYLHLGTTGWLARLTQTDPVGDMPVGTIFRLAGIIAGKTLQVAPVLNAGNILQWALTLVGHRPGEDCAEYFHMAAAEVQGVTVPDGLLFVPYLHAERCPVELPAPRGALLGVTGATTRAQILLAVLEGAALSLRWCAELLGMEKVGLLKVVGGGARSEAWLRMIADNLNVSLLVKPDAHLHPLRGLAALAAVELEWSHSIQDFLREADLREPASNILHPQPCDEGRRRRKFERFKQCVETLGR 499
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----FGGY_N-3kzbA02 A:4-248                                                                                                                                                                                                                               --------FGGY_C-3kzbA01 A:257-450                                                                                                                                                                          ------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhh...hhh.eeeeeeee.eeeeeee.........ee......hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh..eeehhhhhhh..ee....eehhhhhhhh..hhhhh.eee....eeee.hhhhhhhhh.....eee..eehhhhhhhhh.......eeeee...eeeeeeee............eee......eeeeeeee..hhhhhhhhhhhhh......hhhhhhhhhhhh.........eeeee.............eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhh--.........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kzb A   0 SLAFYIATFDIGTTEVKAALADRDGGLHFQRSIALETYGDGNGPVEQDAGDWYDAVQRIASSWWQSGVDARRVSAIVLSGQmQNFLPLDQDHEPLHRAVLYSDKRPLKEAEEINARHGADNLWSALENPmTAASILPKLVFWRASFPQAFGRLRHVVLGAKDYVVLRLTGRHATDRTNASTTGLYRPKDDAWHVELLADYGFSLDLmPRLLEPGEQVGGVSALAARQTGFVSGTPVLCGLGDAGAATLGVGVLDDEDAYLHLGTTGWLARLTQTDPVGDmPVGTIFRLAGIIAGKTLQVAPVLNAGNILQWALTLVGHRPGEDCAEYFHmAAAEVQGVTVPDGLLFVPYLHAERCPVELPAPRGALLGVTGATTRAQILLAVLEGAALSLRWCAELLGmEKVGLLKVVGGGARSEAWLRmIADNLNVSLLVKPDAHLHPLRGLAALAAVELEWSHSIQDFLREADLRE--SNILHPQPCDEGRRRRKFERFKQCVETLGR 499
                                     9        19        29        39        49        59        69        79 |      89        99       109       119       129       139       149       159       169       179       189       199      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       | -|      479       489       499
                                                                                                            81-MSE                                         129-MSE                                                                      206-MSE                                                                  279-MSE                                           329-MSE                                                              398-MSE              419-MSE                                         467  |                             
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                470
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  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 3KZB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q7NWW7_CHRVO | Q7NWW7)
molecular function
    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.
    GO:0004856    xylulokinase activity    Catalysis of the reaction: D-xylulose + ATP = D-xylulose 5-phosphate + ADP + 2 H(+).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    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/TrEMBL
        Q7NWW7_CHRVO | Q7NWW7: 3hz6

(-) Related Entries Specified in the PDB File

3hz6 THE SAME PROTEIN WITHOUT XYLULOSE, PHOSPHATE, GLYCEROL, MALONATE ION BOUND RELATED ID: NYSGXRC-11200B RELATED DB: TARGETDB