Structure of PDB 1dfo Chain A

Receptor sequence
>1dfoA (length=416) Species: 562 (Escherichia coli) [Search protein sequence]
LKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQL
TNKYAEGYPGKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQA
NFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDATG
HIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVDM
AHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYKK
LNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVEV
FLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVPN
DPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIER
IKGKVLDICARYPVYA
3D structure
PDB1dfo Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
ChainA
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y54 E56 D199 T225 K228 R234
Enzyme Commision number 2.1.2.1: glycine hydroxymethyltransferase.
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 PLG A S35 S97 G98 S99 H126 F174 S175 D200 A202 H203 K229 R363 S34 S96 G97 S98 H125 F173 S174 D199 A201 H202 K228 R362
BS02 FFO A L121 G125 H126 L127 S175 N347 S355 P356 F357 L120 G124 H125 L126 S174 N346 S354 P355 F356 PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
BS03 PLG A Y55 Y65 G262 Y54 Y64 G261
BS04 FFO A E57 Y64 Y65 E56 Y63 Y64 PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004372 glycine hydroxymethyltransferase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008732 L-allo-threonine aldolase activity
GO:0016740 transferase activity
GO:0030170 pyridoxal phosphate binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006545 glycine biosynthetic process
GO:0006546 glycine catabolic process
GO:0006564 L-serine biosynthetic process
GO:0006565 L-serine catabolic process
GO:0006730 one-carbon metabolic process
GO:0008652 amino acid biosynthetic process
GO:0019264 glycine biosynthetic process from serine
GO:0035999 tetrahydrofolate interconversion
GO:0046653 tetrahydrofolate metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane

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Cellular Component
External links
PDB RCSB:1dfo, PDBe:1dfo, PDBj:1dfo
PDBsum1dfo
PubMed10656824
UniProtP0A825|GLYA_ECOLI Serine hydroxymethyltransferase (Gene Name=glyA)

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