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(-) Description

Title :  A TRICLINIC CRYSTAL FORM OF E. COLI 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE
 
Authors :  J. Kalinowska-Tluscik, L. Miallau, M. Gabrielsen, G. A. Leonard, S. M. Mcsweeney, W. N. Hunter
Date :  21 Oct 09  (Deposition) - 09 Mar 10  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Non-Mevalonate Pathway, Isoprenoid Biosynthesis, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kalinowska-Tluscik, L. Miallau, M. Gabrielsen, G. A. Leonard, S. M. Mcsweeney, W. N. Hunter
A Triclinic Crystal Form Of Escherichia Coli 4- Diphosphocytidyl-2C-Methyl-D-Erythritol Kinase And Reassessment Of The Quaternary Structure.
Acta Crystallogr. , Sect. F V. 66 237 2010
PubMed-ID: 20208151  |  Reference-DOI: 10.1107/S1744309109054591

(-) Compounds

Molecule 1 - 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE
    Chains: A, B
    EC Number: 2.7.1.148
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CMK, 4-(CYTIDINE-5'-DIPHOSPHO)-2-C-METHYL-D-ERYTHRITOL KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:22 , VAL B:60 , ASN B:65 , LEU B:66 , ILE B:67 , LYS B:96 , GLY B:101 , GLY B:105 , GLY B:107 , SER B:108 , ASN B:110 , HOH B:2207 , HOH B:2208BINDING SITE FOR RESIDUE ADP B1283
2AC2SOFTWAREASN A:65 , LEU A:66 , LYS A:96 , MET A:100 , GLY A:101 , GLY A:105 , GLY A:106 , GLY A:107 , SER A:108 , ASN A:110 , HOH A:2087 , HOH A:2212 , HOH A:2213 , HOH A:2214BINDING SITE FOR RESIDUE ADP A1284
3AC3SOFTWAREASP B:50 , ILE B:51 , HIS B:62 , ARG B:72BINDING SITE FOR RESIDUE GOL B1284

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WW4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:241 -Ala A:242
2Gly B:241 -Ala B:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WW4)

(-) Exons   (0, 0)

(no "Exon" information available for 2WW4)

(-) 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:283
 aligned with ISPE_ECO8A | B7LXC3 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           ISPE_ECO8A     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML 283
               SCOP domains d2ww4a1 A:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d2ww4a2 A:164-283 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                           SCOP domains
               CATH domains 2ww4A01 A:1-164  [code=3.30.230.10, no name defined]                                                                                                                ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee....eee.......hhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eee......eeeee.hhhhhhhhhhhh.....eeeeeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ww4 A   1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML 283
                                    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   


Chain A from PDB  Type:PROTEIN  Length:283
 aligned with ISPE_ECOLI | P62615 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:283
                                    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   
           ISPE_ECOLI     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGANLSPLHRAML 283
               SCOP domains d2ww4a1 A:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d2ww4a2 A:164-283 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                           SCOP domains
               CATH domains 2ww4A01 A:1-164  [code=3.30.230.10, no name defined]                                                                                                                ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee....eee.......hhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eee......eeeee.hhhhhhhhhhhh.....eeeeeee..hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ww4 A   1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAML 283
                                    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   


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with ISPE_ECO8A | B7LXC3 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    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  
           ISPE_ECO8A     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAM 282
               SCOP domains d2ww4b1 B:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d2ww4b2 B:164-282 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                          SCOP domains
               CATH domains 2ww4B01 B:1-164  [code=3.30.230.10, no name defined]                                                                                                                ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------GHMP_kinases_N-2ww4B01 B:91-149                            -----------------------------------------GHMP_kinases_C-2ww4B03 B:191-266                                            ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------GHMP_kinases_N-2ww4B02 B:91-149                            -----------------------------------------GHMP_kinases_C-2ww4B04 B:191-266                                            ---------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee....eee.......hhhhhhhhhhhhhhhhhhhh........eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eee......eeeee.hhhhhhhhhhhhhhhhh.eeeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ww4 B   1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAM 282
                                    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  


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with ISPE_ECOLI | P62615 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    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  
           ISPE_ECOLI     1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGANLSPLHRAM 282
               SCOP domains d2ww4b1 B:1-163 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                                       d2ww4b2 B:164-282 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                          SCOP domains
               CATH domains 2ww4B01 B:1-164  [code=3.30.230.10, no name defined]                                                                                                                ---------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------GHMP_kinases_N-2ww4B01 B:91-149                            -----------------------------------------GHMP_kinases_C-2ww4B03 B:191-266                                            ---------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------GHMP_kinases_N-2ww4B02 B:91-149                            -----------------------------------------GHMP_kinases_C-2ww4B04 B:191-266                                            ---------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee....eee.......hhhhhhhhhhhhhhhhhhhh........eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhh..eeee....eeee......eeeee......hhhhhhh...........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eee......eeeee.hhhhhhhhhhhhhhhhh.eeeeee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ww4 B   1 MRTQWPSPAKLNLFLYITGQRADGYHTLQTLFQFLDYGDTISIELRDDGDIRLLTPVEGVEHEDNLIVRAARLLMKTAADSGRLPTGSGANISIDKRLPMGGGLGGGSSNAATVLVALNHLWQCGLSMDELAEMGLTLGADVPVFVRGHAAFAEGVGEILTPVDPPEKWYLVAHPGVSIPTPVIFKDPELPRNTPKRSIETLLKCEFSNDCEVIARKRFREVDAVLSWLLEYAPSRLTGTGACVFAEFDTESEARQVLEQAPEWLNGFVAKGVNLSPLHRAM 282
                                    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
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)
(-)
Clan: no clan defined [family: GHMP_kinases_C] (13)

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ISPE_ECO8A | B7LXC3)
molecular function
    GO:0050515    4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H(+).
    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: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:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

Chain A,B   (ISPE_ECOLI | P62615)
molecular function
    GO:0050515    4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity    Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H(+).
    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: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:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

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  ISPE_ECOLI | P62615
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 Related Entries

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

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