Structure of PDB 5irp Chain B

Receptor sequence

>5irpB (length=386) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

MIKLCREVWIEVNLDAVKKNLRAIRRHIPHKSKIMAVVKANGYGHGSIEV
ARHALEHGASELAVASVEEGIVLRKAGITAPILVLGFTSLSCVKKSAAWN
ITLSAFQVDWMKEANEILEKEASANRLAIHINVDTGMGRLGVRTKEELLE
VVKALKASKFLRWTGIFTHFSTADEPDTTLTKLQHEKFISFLSFLKKQGI
ELPTVHMCNTAAAIAFPEFSADMIRLGIGLYGLYPSAYIKQLNLVKLEPA
LSLKARIAYVKTMRTEPRTVSYGATYIAEPNEVIATLPIGYADGYSRALS
NRGFVLHRGKRVPVAGRVTMDMIMVSLGENGEGKQGDEVVIYGKQKGAEI
SVDEVAEMLNTINYEVVSTLSRRIPRFYIRDGEIFK

3D structure

• PDB: 5irp Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K39 R139 H169 R225 Y272 T319 D321
• Catalytic site (residue number reindexed from 1): K39 R139 H169 R225 Y272 T319 D321
• Enzyme Commision number: 5.1.1.1: alanine racemase.

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	UAH	B	K39 Y43 L85 R139 H169 N209 T210 R225 G227 I228 Y364	K39 Y43 L85 R139 H169 N209 T210 R225 G227 I228 Y364
BS02	TRS	B	D174 P235 Y364	D174 P235 Y364
BS03	MG	B	L155 K156 S158 L161	L155 K156 S158 L161
BS04	MG	B	A97 N100 R126	A97 N100 R126

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008784 alanine racemase activity
• GO:0016853 isomerase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0006522 alanine metabolic process
• GO:0009252 peptidoglycan biosynthetic process
• GO:0030632 D-alanine biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:5irp, PDBe:5irp, PDBj:5irp
• PDBsum: 5irp
• PubMed: 30977502
• UniProt: P94494|ALR2_BACSU Alanine racemase 2 (Gene Name=alr2)