Structure of PDB 1eqb Chain B

Receptor sequence

>1eqbB (length=417) Species: 562 (Escherichia coli)

MLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQ
LTNKYAEGYPGKRYFGGCEYVDIVEQLAIDRAKELFGADYANVQPHSGSQ
ANFAVYTALLEPGDTVLGMNLAHGGHLTHGSPVNFSGKLYNIVPYGIDAT
GHIDYADLEKQAKEHKPKMIIGGFSAYSGVVDWAKMREIADSIGAYLFVD
MAHVAGLVAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYK
KLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE
VFLERGYKVVSGGTDNHLFLVDLVDKNLTGKEADAALGRANITVNKNSVP
NDPKSPFVTSGIRVGTPAITRRGFKEAEAKELAGWMCDVLDSINDEAVIE
RIKGKVLDICARYPVYA

3D structure

• PDB: 1eqb Role of tyrosine 65 in the mechanism of serine hydroxymethyltransferase.
• Chain: B
• Resolution: 2.7 Å

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	GLY	B	Y55 F65	Y55 F65
BS02	PLP	B	Y55 G262	Y55 G262
BS03	FFO	B	E57 Y64	E57 Y64
BS04	GLY	B	S35 H203 K229 R363	S35 H203 K229 R363
BS05	PLP	B	S97 G98 S99 H126 F174 S175 D200 H203 H228 K229	S97 G98 S99 H126 F174 S175 D200 H203 H228 K229
BS06	FFO	B	L121 G124 G125 H126 L127 S175 N347 S355 P356 F357	L121 G124 G125 H126 L127 S175 N347 S355 P356 F357
BS07	FFO	B	S245 E246	S245 E246

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

External links

• PDB: RCSB:1eqb, PDBe:1eqb, PDBj:1eqb
• PDBsum: 1eqb
• PubMed: 10858298
• UniProt: P0A825|GLYA_ECOLI Serine hydroxymethyltransferase (Gene Name=glyA)