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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM GLYCEROL KINASE WITH ADP
 
Authors :  C. Schnick, S. D. Polley, Q. L. Fivelman, L. Ranford-Cartwright, S. R. Wilkinson, J. A. Brannigan, A. J. Wilkinson, D. A. Baker
Date :  18 Nov 08  (Deposition) - 02 Dec 08  (Release) - 03 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Closed Conformation, Kinase, Malaria, Plasmodium, Transferase, Sugar Kinase/Hsp70/Actin Superfamily, Glycerol Kinase, Open Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Schnick, S. D. Polley, Q. L. Fivelman, L. Ranford-Cartwright, S. R. Wilkinson, J. A. Brannigan, A. J. Wilkinson, D. A. Baker
Structure And Non-Essential Function Of Glycerol Kinase In Plasmodium Falciparum Blood Stages.
Mol. Microbiol. V. 71 533 2009
PubMed-ID: 19040641  |  Reference-DOI: 10.1111/J.1365-2958.2008.06544.X

(-) Compounds

Molecule 1 - GLYCEROL KINASE, PUTATIVE
    Chains: A, B
    EC Number: 2.7.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2X
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO21Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY B:267 , THR B:268 , GLY B:313 , VAL B:316 , PRO B:328 , ALA B:331 , SER B:332 , GLY B:413 , GLY B:414 , MET B:415 , ASN B:418BINDING SITE FOR RESIDUE ADP B1502
02AC2SOFTWAREGLY A:267 , THR A:268 , GLY A:313 , VAL A:316 , PRO A:328 , ALA A:331 , SER A:332 , GLY A:413 , GLY A:414 , MET A:415 , ASN A:418 , HOH A:2145 , HOH A:2146 , HOH A:2147BINDING SITE FOR RESIDUE ADP A1502
03AC3SOFTWAREILE A:309 , THR A:311 , ALA A:312 , PHE A:350 , SER A:351 , GLY A:352 , HOH A:2088 , HOH A:2148 , PHE B:371BINDING SITE FOR RESIDUE EDO A1503
04AC4SOFTWARESER B:10 , THR B:11 , GLN B:12BINDING SITE FOR RESIDUE EDO B1503
05AC5SOFTWAREPHE A:371 , ILE B:309 , THR B:311 , ALA B:312 , PHE B:350 , SER B:351 , GLY B:352 , HOH B:2152 , HOH B:2153BINDING SITE FOR RESIDUE EDO B1504
06AC6SOFTWAREVAL B:72 , ILE B:73 , ILE B:74 , ASP B:234BINDING SITE FOR RESIDUE EDO B1505
07AC7SOFTWARETYR B:293 , LYS B:294 , PHE B:295 , ASP B:299 , LYS B:300 , LYS B:302BINDING SITE FOR RESIDUE EDO B1506
08AC8SOFTWAREARG A:83 , GLU A:84 , ASP A:246 , EDO A:1508BINDING SITE FOR RESIDUE EDO A1504
09AC9SOFTWAREASP A:123 , LYS A:127BINDING SITE FOR RESIDUE EDO A1505
10BC1SOFTWAREILE A:62 , LYS A:66 , VAL A:72 , ILE A:73 , ILE A:74BINDING SITE FOR RESIDUE EDO A1506
11BC2SOFTWAREVAL A:182 , LEU A:196 , ILE A:217 , LYS A:218 , LYS A:294 , ASP A:297 , HOH A:2056BINDING SITE FOR RESIDUE EDO A1507
12BC3SOFTWARETYR B:367 , ARG B:496 , HOH B:2145BINDING SITE FOR RESIDUE EDO B1507
13BC4SOFTWAREGLU A:84 , EDO A:1504 , EDO A:1509BINDING SITE FOR RESIDUE EDO A1508
14BC5SOFTWAREGLU B:84 , TYR B:135 , EDO B:1509 , EDO B:1513 , HOH B:2154BINDING SITE FOR RESIDUE EDO B1508
15BC6SOFTWAREGLN B:82 , ARG B:83 , GLU B:84 , ASP B:246 , EDO B:1508BINDING SITE FOR RESIDUE EDO B1509
16BC7SOFTWAREGLU B:259 , GLY B:277 , GLU B:278 , HOH B:2083BINDING SITE FOR RESIDUE EDO B1510
17BC8SOFTWAREPHE B:388 , ASN B:391 , GLU B:392 , THR B:487 , TRP B:490 , ASN B:491 , HOH B:2155BINDING SITE FOR RESIDUE EDO B1511
18BC9SOFTWARETYR A:135 , EDO A:1508BINDING SITE FOR RESIDUE EDO A1509
19CC1SOFTWAREGLN A:197 , TRP A:198 , ILE A:217BINDING SITE FOR RESIDUE EDO A1510
20CC2SOFTWAREASP A:479 , LYS A:481 , ASP B:479 , ASP B:480 , LYS B:481BINDING SITE FOR RESIDUE EDO A1511
21CC3SOFTWAREGLN B:197 , TRP B:198 , GLU B:216 , ILE B:217BINDING SITE FOR RESIDUE EDO B1512
22CC4SOFTWARESER A:10 , THR A:11 , ASP A:246 , HOH A:2152BINDING SITE FOR RESIDUE EDO A1512
23CC5SOFTWAREEDO B:1508BINDING SITE FOR RESIDUE EDO B1513

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W41)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:355 -Pro A:356
2Ala B:355 -Pro B:356

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W41)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W41)

(-) Exons   (0, 0)

(no "Exon" information available for 2W41)

(-) 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:506
 aligned with Q8IDI4_PLAF7 | Q8IDI4 from UniProtKB/TrEMBL  Length:501

    Alignment length:506
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                 |   5        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       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495      
         Q8IDI4_PLAF7     - -----MNVILSIDQSTQSTKVFFYDEELNIVHSNNLNHEQKCLKPGWYEHDPIEIMTNLYNLMNEGIKVLKDKYTSVIIKCIGITNQRETVIIWDRITGKPLYNAIVWLDTRVEELVTEFSAKYNNNDIQKKTGTYFNTYFSAFKILWLIQNNPEIKQKIDDGTAVIGNINTWLIFNLTKGNCYTDVTNASRTLLMDINTLQWDEKMCKIFNITNMSVLPEIKSNCSNFGLVKSEHVPDYLNIPITGCIGDQQSACIGQAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYALEGSIGTAGSGVSWLLKNKLIDDPSEASDIMEKCENTTGVIFVPAFSGLYAPRWRSDARASIYGMTFNTERSHIVRALLEGIAFQLNEIVDSLTSDMGIEMLHVLRCDGGMTKNKPFMQFNSDIINTKIEVSKYKEVTSLGAAVLAGLEVKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQL 501
               SCOP domains d2w41a1 A:-4-254 automated matches                                                                                                                                                                                                                                 d2w41a2 A:255-501 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee....eeeee.........ee......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh....eeehhhhh............hhhhhhhh...hhhhh.eee..eeeeee.....hhhhh..eeeeeeehhhhhhhhh......eeeeee...eeeeee............eeeeee........eeeeeee....hhhhhhhhhh.....hhhhhhhhhhh......eeee...............eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w41 A  -4 SEFGSMNVILSIDQSTQSTKVFFYDEELNIVHSNNLNHEQKCLKPGWYEHDPIEIMTNLYNLMNEGIKVLKDKYTSVIIKCIGITNQRETVIIWDRITGKPLYNAIVWLDTRVEELVTEFSAKYNNNDIQKKTGTYFNTYFSAFKILWLIQNNPEIKQKIDDGTAVIGNINTWLIFNLTKGNCYTDVTNASRTLLMDINTLQWDEKMCKIFNITNMSVLPEIKSNCSNFGLVKSEHVPDYLNIPITGCIGDQQSACIGQAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYALEGSIGTAGSGVSWLLKNKLIDDPSEASDIMEKCENTTGVIFVPAFSGLYAPRWRSDARASIYGMTFNTERSHIVRALLEGIAFQLNEIVDSLTSDMGIEMLHVLRCDGGMTKNKPFMQFNSDIINTKIEVSKYKEVTSLGAAVLAGLEVKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQL 501
                                     5        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       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495      


Chain B from PDB  Type:PROTEIN  Length:507
 aligned with Q8IDI4_PLAF7 | Q8IDI4 from UniProtKB/TrEMBL  Length:501

    Alignment length:507
                                  1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                  |  4        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       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       
         Q8IDI4_PLAF7     - ------MNVILSIDQSTQSTKVFFYDEELNIVHSNNLNHEQKCLKPGWYEHDPIEIMTNLYNLMNEGIKVLKDKYTSVIIKCIGITNQRETVIIWDRITGKPLYNAIVWLDTRVEELVTEFSAKYNNNDIQKKTGTYFNTYFSAFKILWLIQNNPEIKQKIDDGTAVIGNINTWLIFNLTKGNCYTDVTNASRTLLMDINTLQWDEKMCKIFNITNMSVLPEIKSNCSNFGLVKSEHVPDYLNIPITGCIGDQQSACIGQAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYALEGSIGTAGSGVSWLLKNKLIDDPSEASDIMEKCENTTGVIFVPAFSGLYAPRWRSDARASIYGMTFNTERSHIVRALLEGIAFQLNEIVDSLTSDMGIEMLHVLRCDGGMTKNKPFMQFNSDIINTKIEVSKYKEVTSLGAAVLAGLEVKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQL 501
               SCOP domains d2w41b1 B:-5-254 automated matches                                                                                                                                                                                                                                  d2w41b2 B:255-501 automated matches                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------FGGY_N-2w41B03 B:3-253                                                                                                                                                                                                                                     --------FGGY_C-2w41B01 B:262-454                                                                                                                                                                         ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------FGGY_N-2w41B04 B:3-253                                                                                                                                                                                                                                     --------FGGY_C-2w41B02 B:262-454                                                                                                                                                                         ----------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee....eeeee.........ee......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhh....eeehhhhh............hhhhhhhhh..hhhhh.eee..eeeeee.....hhhhh..eeeeeeehhhhhhhhh......eeeeee...eeeeee............eeeeee........eeeeeee....hhhhhhhhhh.....hhhhhhhhhhh......eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh....hhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w41 B  -5 ISEFGSMNVILSIDQSTQSTKVFFYDEELNIVHSNNLNHEQKCLKPGWYEHDPIEIMTNLYNLMNEGIKVLKDKYTSVIIKCIGITNQRETVIIWDRITGKPLYNAIVWLDTRVEELVTEFSAKYNNNDIQKKTGTYFNTYFSAFKILWLIQNNPEIKQKIDDGTAVIGNINTWLIFNLTKGNCYTDVTNASRTLLMDINTLQWDEKMCKIFNITNMSVLPEIKSNCSNFGLVKSEHVPDYLNIPITGCIGDQQSACIGQAIFDEGEAKCTYGTGVFLLINTGEKVVYSTCGLITTICYKFNDNDKPKYALEGSIGTAGSGVSWLLKNKLIDDPSEASDIMEKCENTTGVIFVPAFSGLYAPRWRSDARASIYGMTFNTERSHIVRALLEGIAFQLNEIVDSLTSDMGIEMLHVLRCDGGMTKNKPFMQFNSDIINTKIEVSKYKEVTSLGAAVLAGLEVKIWDSLDSVKSLLRRSDAVFHSKMDDKKRKKKTSEWNKAVERTLIQL 501
                                     4        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       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W41)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8IDI4_PLAF7 | Q8IDI4)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004370    glycerol kinase activity    Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+).
    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.
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:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0046167    glycerol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    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:0006641    triglyceride metabolic process    The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
cellular component
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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        Q8IDI4_PLAF7 | Q8IDI4: 2w40

(-) Related Entries Specified in the PDB File

2w40 CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM GLYCEROL KINASE WITH BOUND GLYCEROL