7lba | pdb_00007lba

E. coli Agmatinase

spinqualitylabelsall models 7lba, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7lba is a 18 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: MN Gene: speB, WG5_03731 ("Bacillus coli" Migula 1895) Activity: Agmatinase, with EC number 3.5.3.11 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [S0XV43_ECOLX] Catalyzes the formation of putrescine from agmatine.[HAMAP-Rule:MF_01418] Publication Abstract from PubMed Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E. coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P31 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/Rfree values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidic residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion. Structure of the E. coli agmatinase, SPEB.,Chitrakar I, Ahmed SF, Torelli AT, French JB PLoS One. 2021 Apr 15;16(4):e0248991. doi: 10.1371/journal.pone.0248991., eCollection 2021. PMID:33857156 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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