PMID- 29294403
OWN - NLM
STAT- MEDLINE
DCOM- 20191007
LR  - 20191007
IS  - 1095-8657 (Electronic)
IS  - 1047-8477 (Linking)
VI  - 202
IP  - 2
DP  - 2018 May
TI  - Comparative structural and enzymatic studies on Salmonella typhimurium 
      diaminopropionate ammonia lyase reveal its unique features.
PG  - 118-128
LID - S1047-8477(17)30235-6 [pii]
LID - 10.1016/j.jsb.2017.12.012 [doi]
AB  - Cellular metabolism of amino acids is controlled by a large number of pyridoxal 
      5'-phosphate (PLP) dependent enzymes. Diaminopropionate ammonia lyase (DAPAL), a 
      fold type II PLP-dependent enzyme, degrades both the D and L forms of 
      diaminopropionic acid (DAP) to pyruvate and ammonia. Earlier studies on the 
      Escherichia coli DAPAL (EcDAPAL) had suggested that a disulfide bond located 
      close to the active site may be crucial for maintaining the geometry of the 
      substrate entry channel and the active site. In order to obtain further insights 
      into the catalytic properties of DAPAL, structural and functional studies on 
      Salmonella typhimurium DAPAL (StDAPAL) were initiated. The three-dimensional 
      X-ray crystal structure of StDAPAL was determined at 2.5 A resolution. As 
      expected, the polypeptide fold and dimeric organization of StDAPAL is similar to 
      those of EcDAPAL. A phosphate group was located in the active site of StDAPAL and 
      expulsion of this phosphate is probably essential to bring Asp125 to a 
      conformation suitable for proton abstraction from the substrate (D-DAP). The 
      unique disulfide bond of EcDAPAL was absent in StDAPAL, although the enzyme 
      displayed comparable catalytic activity. Site directed mutagenesis of the 
      cysteine residues involved in disulfide bond formation in EcDAPAL followed by 
      functional and biophysical studies further confirmed that the disulfide bond is 
      not necessary either for substrate binding or for catalysis. The activity of 
      StDAPAL but not EcDAPAL was enhanced by monovalent cations suggesting subtle 
      differences in the active site geometries of these two closely related enzymes.
CI  - Copyright (c) 2017 Elsevier Inc. All rights reserved.
FAU - Deka, G
AU  - Deka G
AD  - Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
FAU - Bisht, S
AU  - Bisht S
AD  - Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
FAU - Savithri, H S
AU  - Savithri HS
AD  - Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.
FAU - Murthy, M R N
AU  - Murthy MRN
AD  - Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. 
      Electronic address: mrn@iisc.ac.in.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20171230
PL  - United States
TA  - J Struct Biol
JT  - Journal of structural biology
JID - 9011206
RN  - EC 4.3.1.- (Ammonia-Lyases)
RN  - EC 4.3.1.- (diaminopropionate ammonia-lyase)
SB  - IM
MH  - Ammonia-Lyases/*chemistry/genetics
MH  - Catalysis
MH  - Catalytic Domain/genetics
MH  - Crystallography, X-Ray
MH  - Escherichia coli/*enzymology
MH  - Kinetics
MH  - Mutagenesis, Site-Directed
MH  - Protein Folding
MH  - Salmonella typhimurium/*enzymology
MH  - *Structure-Activity Relationship
MH  - Substrate Specificity
OTO - NOTNLM
OT  - Diaminopropionate ammonia lyase
OT  - Disulfide bond
OT  - Metal ion dependent activity
OT  - PLP
OT  - Phosphate
OT  - X-ray structure
EDAT- 2018/01/03 06:00
MHDA- 2019/10/08 06:00
CRDT- 2018/01/03 06:00
PHST- 2017/10/12 00:00 [received]
PHST- 2017/12/22 00:00 [revised]
PHST- 2017/12/26 00:00 [accepted]
PHST- 2018/01/03 06:00 [pubmed]
PHST- 2019/10/08 06:00 [medline]
PHST- 2018/01/03 06:00 [entrez]
AID - S1047-8477(17)30235-6 [pii]
AID - 10.1016/j.jsb.2017.12.012 [doi]
PST - ppublish
SO  - J Struct Biol. 2018 May;202(2):118-128. doi: 10.1016/j.jsb.2017.12.012. Epub 2017 
      Dec 30.