Structure of PDB 3ukd Chain A

Receptor sequence
>3ukdA (length=191) Species: 44689 (Dictyostelium discoideum) [Search protein sequence]
SKPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSAGDLLRQEQQSGSKDGE
MIATMIKNGEIVPSIVTVKLLKNAIDANQGKNFLVDGFPRNEENNNSWEE
NMKDFVDTKFVLFFDCPEEVMTQRLLKRGESSGRSDDNIESIKKRFNTFN
VQTKLVIDHYNKFDKVKIIPANRDVNEVYNDVENLFKSMGF
3D structure
PDB3ukd Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative.
ChainA
Resolution1.9 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) K19 R93 R131 R137 R148
Catalytic site (residue number reindexed from 1) K16 R90 R128 R134 R145
Enzyme Commision number 2.7.4.14: UMP/CMP kinase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ADP A G16 G18 K19 G20 T21 R127 R131 R176 G13 G15 K16 G17 T18 R124 R128 R173
BS02 C5P A G38 L41 R42 E63 I64 V65 G90 R93 R137 R148 G35 L38 R39 E60 I61 V62 G87 R90 R134 R145
BS03 AF3 A K19 R131 R137 R148 K16 R128 R134 R145
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004127 (d)CMP kinase activity
GO:0005524 ATP binding
GO:0009041 UMP/dUMP kinase activity
GO:0016301 kinase activity
GO:0016776 phosphotransferase activity, phosphate group as acceptor
GO:0019205 nucleobase-containing compound kinase activity
GO:0033862 UMP kinase activity
GO:0036430 CMP kinase activity
GO:0036431 dCMP kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006225 UDP biosynthetic process
GO:0016310 phosphorylation
GO:0043100 pyrimidine nucleobase salvage
GO:0043173 nucleotide salvage
GO:0046705 CDP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
GO:0072528 pyrimidine-containing compound biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Cellular Component
External links
PDB RCSB:3ukd, PDBe:3ukd, PDBj:3ukd
PDBsum3ukd
PubMed9280438
UniProtP20425|KCY_DICDI UMP-CMP kinase (Gene Name=pyrK)

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