SASDC58: Dipeptidyl peptidase III: pgDPP3_FL (Peptidase, M49 family, PgDPP3)

Basic information

• Entry: Database: SASBDB / ID: SASDC58

Sample

Dipeptidyl peptidase III: pgDPP3_FL

• Peptidase, M49 family (protein), PgDPP3, Porphyromonas gingivalis (strain ATCC BAA-308 / W83)

• Function / homology: Peptidase family M49 / Peptidase family M49 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / hydrolase activity / metal ion binding / Peptidase, M49 family
• Biological species: Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
• Citation: Journal: PLoS One / Year: 2017; Title: A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain.; Authors: Altijana Hromić-Jahjefendić / Nina Jajčanin Jozić / Saša Kazazić / Marina Grabar Branilović / Zrinka Karačić / Jörg H Schrittwieser / Krishna Mohan Padmanabha Das / Marko Tomin / Monika Oberer / Karl Gruber / Marija Abramić / Sanja Tomić / ; Abstract: Porphyromonas gingivalis, an asaccharolytic Gram-negative oral anaerobe, is a major pathogen associated with adult periodontitis, a chronic infective disease that a significant percentage of the human population suffers from. It preferentially utilizes dipeptides as its carbon source, suggesting the importance of dipeptidyl peptidase (DPP) types of enzyme for its growth. Until now DPP IV, DPP5, 7 and 11 have been extensively investigated. Here, we report the characterization of DPP III using molecular biology, biochemical, biophysical and computational chemistry methods. In addition to the expected evolutionarily conserved regions of all DPP III family members, PgDPP III possesses a C-terminal extension containing an Armadillo (ARM) type fold similar to the AlkD family of bacterial DNA glycosylases, implicating it in alkylation repair functions. However, complementation assays in a DNA repair-deficient Escherichia coli strain indicated the absence of alkylation repair function for PgDPP III. Biochemical analyses of recombinant PgDPP III revealed activity similar to that of DPP III from Bacteroides thetaiotaomicron, and in the range between activities of human and yeast counterparts. However, the catalytic efficiency of the separately expressed DPP III domain is ~1000-fold weaker. The structure and dynamics of the ligand-free enzyme and its complex with two different diarginyl arylamide substrates was investigated using small angle X-ray scattering, homology modeling, MD simulations and hydrogen/deuterium exchange (HDX). The correlation between the experimental HDX and MD data improved with simulation time, suggesting that the DPP III domain adopts a semi-closed or closed form in solution, similar to that reported for human DPP III. The obtained results reveal an atypical DPP III with increased structural complexity: its superhelical C-terminal domain contributes to peptidase activity and influences DPP III interdomain dynamics. Overall, this research reveals multifunctionality of PgDPP III and opens direction for future research of DPP III family proteins.

Contact author

• Krishna Mohan Padmanabha Das (university of graz)

Models

• Model #1600: ; Type: dummy / Radius of dummy atoms: 3.40 A / Chi-square value: 0.636 / P-value: 0.052255; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Dipeptidyl peptidase III: pgDPP3_FL / Specimen concentration: 1.02-8.80
• Buffer: Name: 50mM Tris,100mM NaCl / pH: 8

Entity #822

Name: PgDPP3 / Type: protein / Description: Peptidase, M49 family / Formula weight: 101.655 / Num. of mol.: 1
Source: Porphyromonas gingivalis (strain ATCC BAA-308 / W83)
References: UniProt: Q7MX92
Sequence:

MTKETTQHRS GERVARFADI EVLSYRADLF GTLTPKQRML CYHLSEAALR GRDITTIQNC RYNLWVRSLM ERIYTHLSKS ERTDDFALLE EYLFCIWFAN GIHHHYSGAK FIARFSPEFL REALRVTGVE LEPEEQALLE RVLYDTDFLP KQTEQSGEED IIKASSVNFY APGITRAEAE SHYKNLIEAL PENERSCPPS FGLNTRLIRS TSGELKDEVC CIDGLYSPAI EAVVASLEAA IPYTENEEQA ACIRLLCDYY RTGDVRLYDR FCIRWVENNR TRIDFINGFT EVYADPIGIH GSWEGLVHMQ DEEAGRRTRI ISEHAGWFEA HSPIDARFRK KNPHGISATV VNVLTIAGDS YPATPIGINL PNADWIRAEH GSKSVTIDNI TDAYNHAARG TGLYEEFIPD EEVRRHVELH ADLTDSLHTD LHECLGHGSG QLLPGVPGDA LGEHASTLEE TRADLFALYF LADPKMIELG LLTDPDAYKA NYYKYMLNGL MTQLVRIKRG EEIEEAHMRN RALIARYVLE HAERPGAMSL VCEEGKTALV IKDYEAVRAI IAGLLTEVQR IKSEGDYTAG KALVERYAVH VDPLLHEEVL MRYAKLDIAP YKGFVNPRLR PVYNSEGRLT DATIEYTEGY AEQMLRYSAE YSFLPTDSPL LQEARRLRSH LRRAMDGVLS ASMREKGLHY GINFGVTREH LLRLARTADA SAPLADYLWR RDVRETKILA TMIFPAEELT HEQATRFLRE ADNVELREQL TANLLERMPE AIRSIGRWIE SKETTPDMMT GVLTLAARLF TRGIFPENAP AEKLLALAIL HLSDEEQKTE LRRASALLLK RYGRGSAERT KKVLCLLPES SQDTAPVLYE LCEDIRFELD FYPKDEHHHH HH

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.5 mm
• Detector: Name: Pilatus 1M

Scan

Title: Dipeptidyl peptidase III: pgDPP3_FL / Measurement date: Mar 14, 2015 / Storage temperature: 4 °C / Cell temperature: 4 °C / Number of frames: 8 / Unit: 1/nm /

	Min	Max
Q	0.1333	4.8187

Distance distribution function P(R)

Sofotware P(R): GNOM 4.6 / Number of points: 480 /

	Min	Max
Q	0.2352	4.778
P(R) point	22	501
R	0	11.25

Result

Type of curve: merged

	Experimental	Standard	Porod
MW	101 kDa	101 kDa	72 kDa
Volume	-	-	116 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	71.02	0.185	70.244	0.289
Radius of gyration, Rg	3.08 nm	0.012	3 nm	0.018

	Min	Max
D	-	11.25
Guinier point	22	64