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* Residue conservation analysis
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PDB id:
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Transferase
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Title:
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Crystal structure of the streptococcus pneumoniae phosphomevalonate kinase (pmk)
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Structure:
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Phosphomevalonate kinase. Chain: a, b, c, d, e, f. Engineered: yes
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Source:
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Streptococcus pneumoniae r6. Organism_taxid: 171101. Strain: atcc baa-255 / r6. Gene: mvak2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
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Biol. unit:
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Dimer (from
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Resolution:
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2.42Å
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R-factor:
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0.215
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R-free:
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0.257
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Authors:
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M.J.Romanowski,J.B.Bonanno,S.K.Burley,New York Sgx Research Center For Structural Genomics (Nysgxrc)
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Key ref:
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M.J.Romanowski
et al.
(2002).
Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.
Proteins,
47,
568-571.
PubMed id:
DOI:
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Date:
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05-Oct-01
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Release date:
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08-May-02
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PROCHECK
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Headers
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References
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Q8DR49
(Q8DR49_STRR6) -
Phosphomevalonate kinase
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Seq:
Struc:
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335 a.a.
322 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Gene Ontology (GO) functional annotation
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Biological process
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phosphorylation
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1 term
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Biochemical function
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nucleotide binding
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4 terms
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DOI no:
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Proteins
47:568-571
(2002)
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PubMed id:
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Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.
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M.J.Romanowski,
J.B.Bonanno,
S.K.Burley.
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ABSTRACT
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Selected figure(s)
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Figure 1.
Figure 1. Alignment of S. pneumoniae PMK homologs and related
proteins identified during an iterative PSI-BLAST[14] search (20
iterations; January 2002). The secondary structural elements are
shown above the aligned sequences. Gray spheres represent
disordered residues. Color-coding denotes sequence conservation
among the proteins (white-to-green ramp, 30-100% identity).
PMKSTRPN ( ), S. pneumoniae (strain R6) PMK; PMKSTRPY
(GI:9937402), Streptococcus pyogenes PMK (Z-score = 2e-77; 50%
identity); PMKENTFC (GI:9937388), Enterococcus faecalis PMK
(Z-score = 2e-81; 29% identity); PMKLISIN (GI:16799091),
putative Listeria innocua PMK (Z-score = 3e-68; 28% identity);
PMKSTAHA (GI: 9937374), Staphylococcus haemolyticus PMK (Z-score
= 8e-85; 29% identity); PMKSTAUR (GI: 9937366), S. aureus PMK
(Z-score = 2e-84; 26% identity); MvKMETJA (GI: 15669275), M.
jannaschii MK (Z-score = 1e-57; 21% identity), MvKENTFC (GI:
9937386), E. faecalis MK (Z-score = 6e-66; 18% identity).
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Figure 2.
Figure 2. RIBBONS[15] drawing of PMK with labeled N- and
C-termini and secondary structural elements color-coded for  -helices
(blue) and  -strands
(red). Motifs I, II, and III lining the putative active site
cleft are shown in green.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2002,
47,
568-571)
copyright 2002.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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C.Fan,
H.J.Fromm,
and
T.A.Bobik
(2009).
Kinetic and functional analysis of L-threonine kinase, the PduX enzyme of Salmonella enterica.
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J Biol Chem, 284,
20240-20248.
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J.L.Andreassi,
M.W.Vetting,
P.W.Bilder,
S.L.Roderick,
and
T.S.Leyh
(2009).
Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family.
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Biochemistry, 48,
6461-6468.
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PDB code:
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C.Q.Diep,
X.Tao,
V.Pilauri,
M.Losiewicz,
T.E.Blank,
and
J.E.Hopper
(2008).
Genetic evidence for sites of interaction between the Gal3 and Gal80 proteins of the Saccharomyces cerevisiae GAL gene switch.
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Genetics, 178,
725-736.
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T.J.Herdendorf,
and
H.M.Miziorko
(2007).
Functional evaluation of conserved basic residues in human phosphomevalonate kinase.
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Biochemistry, 46,
11780-11788.
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T.Sgraja,
T.K.Smith,
and
W.N.Hunter
(2007).
Structure, substrate recognition and reactivity of Leishmania major mevalonate kinase.
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BMC Struct Biol, 7,
20.
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PDB codes:
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C.Q.Diep,
G.Peng,
M.Bewley,
V.Pilauri,
I.Ropson,
and
J.E.Hopper
(2006).
Intragenic suppression of Gal3C interaction with Gal80 in the Saccharomyces cerevisiae GAL gene switch.
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Genetics, 172,
77-87.
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J.B.Thoden,
and
H.M.Holden
(2005).
The molecular architecture of human N-acetylgalactosamine kinase.
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J Biol Chem, 280,
32784-32791.
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PDB codes:
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P.Acharya,
M.Goenrich,
C.H.Hagemeier,
U.Demmer,
J.A.Vorholt,
R.K.Thauer,
and
U.Ermler
(2005).
How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1.
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J Biol Chem, 280,
13712-13719.
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PDB codes:
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S.S.Doun,
J.W.Burgner,
S.D.Briggs,
and
V.W.Rodwell
(2005).
Enterococcus faecalis phosphomevalonate kinase.
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Protein Sci, 14,
1134-1139.
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M.Hedl,
and
V.W.Rodwell
(2004).
Enterococcus faecalis mevalonate kinase.
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Protein Sci, 13,
687-693.
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N.Fernandez-Fuentes,
A.Hermoso,
J.Espadaler,
E.Querol,
F.X.Aviles,
and
B.Oliva
(2004).
Classification of common functional loops of kinase super-families.
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Proteins, 56,
539-555.
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S.C.Sinha,
B.N.Chaudhuri,
J.W.Burgner,
G.Yakovleva,
V.J.Davisson,
and
J.L.Smith
(2004).
Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.
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J Biol Chem, 279,
15491-15498.
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PDB code:
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D.J.Timson,
and
R.J.Reece
(2003).
Functional analysis of disease-causing mutations in human galactokinase.
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Eur J Biochem, 270,
1767-1774.
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D.Pilloff,
K.Dabovic,
M.J.Romanowski,
J.B.Bonanno,
M.Doherty,
S.K.Burley,
and
T.S.Leyh
(2003).
The kinetic mechanism of phosphomevalonate kinase.
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J Biol Chem, 278,
4510-4515.
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H.M.Holden,
I.Rayment,
and
J.B.Thoden
(2003).
Structure and function of enzymes of the Leloir pathway for galactose metabolism.
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J Biol Chem, 278,
43885-43888.
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J.B.Thoden,
and
H.M.Holden
(2003).
Molecular structure of galactokinase.
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J Biol Chem, 278,
33305-33311.
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PDB code:
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J.G.Luz,
C.A.Hassig,
C.Pickle,
A.Godzik,
B.J.Meyer,
and
I.A.Wilson
(2003).
XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators.
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Genes Dev, 17,
977-990.
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PDB code:
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L.Miallau,
M.S.Alphey,
L.E.Kemp,
G.A.Leonard,
S.M.McSweeney,
S.Hecht,
A.Bacher,
W.Eisenreich,
F.Rohdich,
and
W.N.Hunter
(2003).
Biosynthesis of isoprenoids: crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol kinase.
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Proc Natl Acad Sci U S A, 100,
9173-9178.
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PDB code:
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T.Wada,
T.Kuzuyama,
S.Satoh,
S.Kuramitsu,
S.Yokoyama,
S.Unzai,
J.R.Tame,
and
S.Y.Park
(2003).
Crystal structure of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
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J Biol Chem, 278,
30022-30027.
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PDB code:
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S.K.Burley,
and
J.B.Bonanno
(2002).
Structuring the universe of proteins.
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Annu Rev Genomics Hum Genet, 3,
243-262.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
