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(-) Description

Title :  THE CRYSTAL STRUCTURE OF XLYLULOSE KINASE FROM YERSINIA PSEUDOTUBERCULOSIS
 
Authors :  Z. Zhang, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  10 Dec 09  (Deposition) - 05 Jan 10  (Release) - 12 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Xlylulose Kinase, Sgx, Psi, Kinase, Structural Genomics, 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
The Crystal Structure Of Xylulose Kinase From Yersinia Pseudotuberculosis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLULOSE KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21 (DE3) CODON+RIL STRATAGENE
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ARAB2, Y0231,YPTB3592, YP_3910
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633
    Synonym: PUTATIVE CARBOHYDRATE KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 51)

Asymmetric Unit (4, 51)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE48Mod. Amino AcidSELENOMETHIONINE
4XUL1Ligand/IonD-XYLULOSE
Biological Unit 1 (4, 51)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE48Mod. Amino AcidSELENOMETHIONINE
4XUL1Ligand/IonD-XYLULOSE
Biological Unit 2 (3, 26)
No.NameCountTypeFull Name
1EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2GOL1Ligand/IonGLYCEROL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4XUL-1Ligand/IonD-XYLULOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:81 , CYS A:82 , TRP A:109 , LYS A:187 , ASP A:255 , ALA A:256 , HIS A:257 , SER A:287 , GLU A:319 , ARG A:388 , HOH A:897BINDING SITE FOR RESIDUE XUL A 553
2AC2SOFTWARETHR B:81 , CYS B:82 , TRP B:109 , ASP B:255 , GLY B:285 , THR B:286 , SER B:287 , MSE B:477 , HOH B:790BINDING SITE FOR RESIDUE EPE B 553
3AC3SOFTWAREPRO A:454 , HOH A:841 , HOH A:859 , HOH A:926 , PRO B:153 , ASN B:154 , HOH B:806BINDING SITE FOR RESIDUE GOL B 554

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L0Q)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:305 -Pro A:306
2Ser A:389 -Pro A:390
3Gly B:305 -Pro B:306
4Ser B:389 -Pro B:390

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L0Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L0Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3L0Q)

(-) 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:541
 aligned with Q665C6_YERPS | Q665C6 from UniProtKB/TrEMBL  Length:545

    Alignment length:541
                                    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       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541 
         Q665C6_YERPS     2 ASYFIGVDVGTGSARAGVFDLQGRMVGQASREITMFKPKADFVEQSSENIWQAVCNAVRDAVNQADINPIQVKGLGFDATCSLVVLDKEGNPLTVSPSGRNEQNVIVWMDHRAITQAERINATKHPVLEFVGGVISPEMQTPKLLWLKQHMPNTWSNVGHLFDLPDFLTWRATKDETRSLCSTVCKWTYLGHEDRWDPSYFKLVGLADLLDNNAAKIGATVKPMGAPLGHGLSQRAASEMGLIPGTAVSVSIIDAHAGTIGILGASGVTGENANFDRRIALIGGTSTAHMAMSRSAHFISGIWGPYYSAILPEYWLNEGGQSATGALIDHIIQSHPCYPALLEQAKNKGETIYEALNYILRQMAGEPENIAFLTNDIHMLPYFHGNRSPRANPNLTGIITGLKLSTTPEDMALRYLATIQALALGTRHIIETMNQNGYNIDTMMASGGGTKNPIFVQEHANATGCAMLLPEESEAMLLGSAMMGTVAAGVFESLPEAMAAMSRIGKTVTPQTNKIKAYYDRKYRVFHQMYHDHMRYQALMQ 542
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee....eeeeeeee...eeee..eeeehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee...eeeee.................ee......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhheeeeeehhhhhhhhhhh...eehhhhhhhh.........hhhhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhh.....ee...eehhhhhhhhhh..............eeeee....eeeeeee.........eeeee.......eeeeeee..hhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...ee.................ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0q A   2 ASYFIGVDVGTGSARAGVFDLQGRmVGQASREITmFKPKADFVEQSSENIWQAVCNAVRDAVNQADINPIQVKGLGFDATCSLVVLDKEGNPLTVSPSGRNEQNVIVWmDHRAITQAERINATKHPVLEFVGGVISPEmQTPKLLWLKQHmPNTWSNVGHLFDLPDFLTWRATKDETRSLCSTVCKWTYLGHEDRWDPSYFKLVGLADLLDNNAAKIGATVKPmGAPLGHGLSQRAASEmGLIPGTAVSVSIIDAHAGTIGILGASGVTGENANFDRRIALIGGTSTAHmAmSRSAHFISGIWGPYYSAILPEYWLNEGGQSATGALIDHIIQSHPCYPALLEQAKNKGETIYEALNYILRQmAGEPENIAFLTNDIHmLPYFHGNRSPRANPNLTGIITGLKLSTTPEDmALRYLATIQALALGTRHIIETmNQNGYNIDTmmASGGGTKNPIFVQEHANATGCAmLLPEESEAmLLGSAmmGTVAAGVFESLPEAmAAmSRIGKTVTPQTNKIKAYYDRKYRVFHQmYHDHmRYQALmQ 542
                                    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       311       321       331       341       351       361  |    371       381       391       401       411|      421       431  |    441  ||   451       461      |471     | 481 ||    491       501|      511       521       531   |   541 
                                                   26-MSE    36-MSE                                                                   110-MSE                       140-MSE     152-MSE                                                                  225-MSE         241-MSE                                           291-MSE                                                                  364-MSE         380-MSE                         412-MSE               434-MSE   444-MSE                 468-MSE  477-MSE ||            499-MSE                        530-MSE|     | 
                                                                                                                                                                                                                                                                                                                             293-MSE                                                                                                                                                 445-MSE                               483-MSE            502-MSE                          535-MSE | 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            484-MSE                                                  541-MSE

Chain B from PDB  Type:PROTEIN  Length:542
 aligned with Q665C6_YERPS | Q665C6 from UniProtKB/TrEMBL  Length:545

    Alignment length:542
                                    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       490       500       510       520       530       540  
         Q665C6_YERPS     1 MASYFIGVDVGTGSARAGVFDLQGRMVGQASREITMFKPKADFVEQSSENIWQAVCNAVRDAVNQADINPIQVKGLGFDATCSLVVLDKEGNPLTVSPSGRNEQNVIVWMDHRAITQAERINATKHPVLEFVGGVISPEMQTPKLLWLKQHMPNTWSNVGHLFDLPDFLTWRATKDETRSLCSTVCKWTYLGHEDRWDPSYFKLVGLADLLDNNAAKIGATVKPMGAPLGHGLSQRAASEMGLIPGTAVSVSIIDAHAGTIGILGASGVTGENANFDRRIALIGGTSTAHMAMSRSAHFISGIWGPYYSAILPEYWLNEGGQSATGALIDHIIQSHPCYPALLEQAKNKGETIYEALNYILRQMAGEPENIAFLTNDIHMLPYFHGNRSPRANPNLTGIITGLKLSTTPEDMALRYLATIQALALGTRHIIETMNQNGYNIDTMMASGGGTKNPIFVQEHANATGCAMLLPEESEAMLLGSAMMGTVAAGVFESLPEAMAAMSRIGKTVTPQTNKIKAYYDRKYRVFHQMYHDHMRYQALMQ 542
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---FGGY_N-3l0qB03 B:4-262                                                                                                                                                                                                                                             -----------------FGGY_C-3l0qB01 B:280-489                                                                                                                                                                                          ----------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---FGGY_N-3l0qB04 B:4-262                                                                                                                                                                                                                                             -----------------FGGY_C-3l0qB02 B:280-489                                                                                                                                                                                          ----------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee...eeeee.................ee......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhheeeeeehhhhhhhhhhh...eehhhhhhhh.........hhhhhhhhhhhhhhhhhhh.....ee..........hhhhhhhhh.....ee...eehhhhhhhhhhh.............eeeee....eeeeeee.........eeeee.......eeeeeee..hhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...ee.................ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l0q B   1 LASYFIGVDVGTGSARAGVFDLQGRmVGQASREITmFKPKADFVEQSSENIWQAVCNAVRDAVNQADINPIQVKGLGFDATCSLVVLDKEGNPLTVSPSGRNEQNVIVWmDHRAITQAERINATKHPVLEFVGGVISPEmQTPKLLWLKQHmPNTWSNVGHLFDLPDFLTWRATKDETRSLCSTVCKWTYLGHEDRWDPSYFKLVGLADLLDNNAAKIGATVKPmGAPLGHGLSQRAASEmGLIPGTAVSVSIIDAHAGTIGILGASGVTGENANFDRRIALIGGTSTAHmAmSRSAHFISGIWGPYYSAILPEYWLNEGGQSATGALIDHIIQSHPCYPALLEQAKNKGETIYEALNYILRQmAGEPENIAFLTNDIHmLPYFHGNRSPRANPNLTGIITGLKLSTTPEDmALRYLATIQALALGTRHIIETmNQNGYNIDTmmASGGGTKNPIFVQEHANATGCAmLLPEESEAmLLGSAmmGTVAAGVFESLPEAmAAmSRIGKTVTPQTNKIKAYYDRKYRVFHQmYHDHmRYQALmQ 542
                                    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  ||   490       500 |     510       520       530    |  540| 
                                                    26-MSE    36-MSE                                                                   110-MSE                       140-MSE     152-MSE                                                                  225-MSE         241-MSE                                           291-MSE                                                                  364-MSE         380-MSE                         412-MSE               434-MSE   444-MSE                 468-MSE  477-MSE ||            499-MSE                        530-MSE|     | 
                                                                                                                                                                                                                                                                                                                              293-MSE                                                                                                                                                 445-MSE                               483-MSE            502-MSE                          535-MSE | 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             484-MSE                                                  541-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  (0, 0)

(no "SCOP Domain" information available for 3L0Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L0Q)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q665C6_YERPS | Q665C6)
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: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: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: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
        Q665C6_YERPS | Q665C6: 3gg4

(-) Related Entries Specified in the PDB File

3gg4 RELATED ID: NYSGXRC-11200D RELATED DB: TARGETDB