Structure of PDB 1dfo Chain B

Receptor sequence
>1dfoB (length=417) Species: 562 (Escherichia coli) [Search protein sequence]
MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQ
LTNKYAEGYPGKRYYGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQ
ANFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDAT
GHIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVD
MAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYK
KLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE
VFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVP
NDPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIE
RIKGKVLDICARYPVYA
3D structure
PDB1dfo Crystal structure at 2.4 A resolution of E. coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate.
ChainB
Resolution2.4 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) Y55 E57 D200 T226 K229 R235
Catalytic site (residue number reindexed from 1) Y55 E57 D200 T226 K229 R235
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 B Y55 Y65 G262 Y55 Y65 G262
BS02 FFO B E57 Y64 Y65 E57 Y64 Y65 PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
BS03 PLG B S35 S97 G98 S99 H126 F174 S175 D200 A202 H203 K229 R363 S35 S97 G98 S99 H126 F174 S175 D200 A202 H203 K229 R363
BS04 FFO B L121 G125 H126 L127 S175 N347 S355 P356 F357 L121 G125 H126 L127 S175 N347 S355 P356 F357 PDBbind-CN: -logKd/Ki=6.70,Ki=0.2uM
BS05 FFO B S245 E247 S245 E247 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1dfo, PDBe:1dfo, PDBj:1dfo
PDBsum1dfo
PubMed10656824
UniProtP0A825|GLYA_ECOLI Serine hydroxymethyltransferase (Gene Name=glyA)

[Back to BioLiP]