5X49 | pdb_00005x49

Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3)

PDB DOI: https://doi.org/10.2210/pdb5X49/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-02-10 Released: 2017-05-17
Deposition Author(s): Singh, R., Kumar, A., Ghosh, B., Jamdar, S., Makde, R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.177 (Depositor), 0.180 (DCC)
R-Value Work:
0.154 (Depositor), 0.156 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes.

Singh, R., Jamdar, S.N., Goyal, V.D., Kumar, A., Ghosh, B., Makde, R.D.

(2017) J Biological Chem 292: 10035-10047

PubMed: 28476889 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M117.783357
Primary Citation Related Structures:
5X49

PubMed Abstract:
The human aminopeptidase XPNPEP3 is associated with cystic kidney disease and TNF-TNFR2 cellular signaling. Its yeast and plant homolog Icp55 processes several imported mitochondrial matrix proteins leading to their stabilization. However, the molecular basis for the diverse roles of these enzymes in the cell is unknown. Here, we report the crystal structure of human XPNPEP3 with bound apstatin product at 1.65 Å resolution, and we compare its in vitro substrate specificity with those of fungal Icp55 enzymes. In contrast to the suggestions by earlier in vivo studies of mitochondrial processing, we found that these enzymes are genuine Xaa-Pro aminopeptidases, which hydrolyze peptides with proline at the second position (P1'). The mitochondrial processing activity involving cleavage of peptides lacking P1' proline was also detected in the purified enzymes. A wide proline pocket as well as molecular complementarity and capping at the S1 substrate site of XPNPEP3 provide the necessary structural features for processing the mitochondrial substrates. However, this activity was found to be significantly lower as compared with Xaa-Pro aminopeptidase activity. Because of similar activity profiles of Icp55 and XPNPEP3, we propose that XPNPEP3 plays the same mitochondrial role in humans as Icp55 does in yeast. Both Xaa-Pro aminopeptidase and mitochondrial processing activities of XPNPEP3 have implications toward mitochondrial fitness and cystic kidney disease. Furthermore, the presence of both these activities in Icp55 elucidates the unexplained processing of the mitochondrial cysteine desulfurase Nfs1 in yeast. The enzymatic and structural analyses reported here provide a valuable molecular framework for understanding the diverse cellular roles of XPNPEP3.

Organizational Affiliation

From the High Pressure and Synchrotron Radiation Physics Division and.

Macromolecule Content

Total Structure Weight: 104.9 kDa
Atom Count: 8,041
Modeled Residue Count: 882
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable Xaa-Pro aminopeptidase 3	A, B	456	Homo sapiens	Mutation(s): 0 Gene Names: XPNPEP3 EC: 3.4.11.9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQH7 (Homo sapiens) Explore Q9NQH7 Go to UniProtKB: Q9NQH7
PHAROS: Q9NQH7 GTEx: ENSG00000196236
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NQH7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P Query on 12P Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
01B Query on 01B Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	(2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid C₁₀ H₁₃ N O₃ LDSJMFGYNFIFRK-BDAKNGLRSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	G [auth A] H [auth A] I [auth A] O [auth B] P [auth B] G [auth A], H [auth A], I [auth A], O [auth B], P [auth B], Q [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain R [auth B]	J [auth A], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	C [auth A], D [auth A], K [auth B], L [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.177 (Depositor), 0.180 (DCC)
R-Value Work: 0.154 (Depositor), 0.156 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.897	α = 90
b = 135.103	β = 99.87
c = 67.205	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHENIX	model building
PHASER	phasing
Aimless	data processing
XDS	data processing
MAR345dtb	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-05-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-05-17
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2023-11-22
Changes: Refinement description