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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO E. COLI XYLULOSE KINASE
 
Authors :  E. Di Luccio, J. Voegtli, D. K. Wilson
Date :  20 Oct 06  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Xylulokinase, Fggy Kinase, Atpase, Xylulose, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Di Luccio, B. Petschacher, J. Voegtli, H. T. Chou, H. Stahlberg, B. Nidetzky, D. K. Wilson
Structural And Kinetic Studies Of Induced Fit In Xylulose Kinase From Escherichia Coli.
J. Mol. Biol. V. 365 783 2007
PubMed-ID: 17123542  |  Reference-DOI: 10.1016/J.JMB.2006.10.068
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLULOSE KINASE
    Chains: A, B
    EC Number: 2.7.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB2
    Expression System Strain: BL21*
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: XYLB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: XYLULOKINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2NLX)

(-) Sites  (0, 0)

(no "Site" information available for 2NLX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NLX)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu B:292 -Ser B:293
2Glu B:325 -Pro B:326
3Gln B:344 -Ala B:345

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NLX)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FGGY_KINASES_1PS00933 FGGY family of carbohydrate kinases signature 1.XYLB_ECOLI126-138
 		  2A:126-138
B:126-138
2FGGY_KINASES_2PS00445 FGGY family of carbohydrate kinases signature 2.XYLB_ECOLI347-367
 		  2A:347-367
B:347-367

(-) Exons   (0, 0)

(no "Exon" information available for 2NLX)

(-) 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:476
 aligned with XYLB_ECOLI | P09099 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:484
                                    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       390       400       410       420       430       440       450       460       470       480    
           XYLB_ECOLI     1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPLMA 484
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh......eeeeee.....eee.........ee......hhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhh..eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee....eeee.hhhhhhhh.....eee..eehhhhhhhhhh.....eeeeee...eeeeee............eeee......eeeeeee....hhhhhhhhhh...hhhhhhhhhh.........eeeeee.--------..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh...hhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nlx A   1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLS--------PQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPLMA 484
                                    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   |     -  |    350       360       370       380       390       400       410       420       430       440       450       460       470       480    
                                                                                                                                                                                                                                                                                                                                                                       334      343                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:472
 aligned with XYLB_ECOLI | P09099 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:482
                                    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       390       400       410       420       430       440       450       460       470       480  
           XYLB_ECOLI     1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPL 482
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) FGGY_N-2nlxB03 B:1-240                                                                                                                                                                                                                          --------FGGY_C-2nlxB01 B:249-436                                                                                                                                                                    ---------------------------------------------- Pfam domains (1)
           Pfam domains (2) FGGY_N-2nlxB04 B:1-240                                                                                                                                                                                                                          --------FGGY_C-2nlxB02 B:249-436                                                                                                                                                                    ---------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh......eeeeee.....eee.........ee......hhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhhhhhhhhh..eeehhhhhhhhhhhh..eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee....eeee.hhhhhhhh.....eee..eehhhhhhhhh.......eeee....eeeeeee..........eeeee......eeeeeee...hhhhhhhhhhh...hhhhhhhhhhhh.............----------.............hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhh...hhhhhh....eeeee..hhhhhhhhhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nlx B   1 MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALGDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYL----------QAKGVFFGLTHQHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQLLPL 482
                                    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  |      -   |   350       360       370       380       390       400       410       420       430       440       450       460       470       480  
                                                                                                                                                                                                                                                                                                                                                                      333        344
   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  (0, 0)

(no "SCOP Domain" information available for 2NLX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2NLX)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (XYLB_ECOLI | P09099)
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.
    GO:0004856    xylulokinase activity    Catalysis of the reaction: D-xylulose + ATP = D-xylulose 5-phosphate + ADP + 2 H(+).
biological process
    GO:0042843    D-xylose catabolic process    The chemical reactions and pathways resulting in the breakdown of D-xylose, a naturally occurring plant polysaccharide.
    GO:0042732    D-xylose metabolic process    The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.
    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.
    GO:0005998    xylulose catabolic process    The chemical reactions and pathways resulting in the breakdown of xylulose, the ketopentose threo-2-pentulose.
    GO:0005997    xylulose metabolic process    The chemical reactions and pathways involving xylulose, the ketopentose threo-2-pentulose.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
    Gln B:344 - Ala B:345   [ RasMol ]  
    Glu B:325 - Pro B:326   [ RasMol ]  
    Leu B:292 - Ser B:293   [ RasMol ]  
 

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  2.7.1.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYLB_ECOLI | P09099: 2itm

(-) Related Entries Specified in the PDB File

2itm CRYSTAL STRUCTURE OF THE E. COLI XYLULOSE KINASE COMPLEXED WITH XYLULOSE