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 1PQ3 | pdb_00001pq3

Human Arginase II: Crystal Structure and Physiological Role in Male and Female Sexual Arousal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.247 (Depositor) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PQ3

This is version 1.3 of the entry. See complete history. 

Literature

Human Arginase II: Crystal Structure and Physiological Role in Male and Female Sexual Arousal

Cama, E., Colleluori, D.M., Emig, F.A., Shin, H., Kim, S.W., Kim, N.N., Traish, A.M., Ash, D.E., Christianson, D.W.

(2003) Biochemistry 42: 8445-8451

  • DOI: https://doi.org/10.1021/bi034340j
  • Primary Citation Related Structures: 
    1PQ3

  • PubMed Abstract: 

    Arginase is a binuclear manganese metalloenzyme that catalyzes the hydrolysis of l-arginine to form l-ornithine and urea. The X-ray crystal structure of a fully active, truncated form of human arginase II complexed with a boronic acid transition state analogue inhibitor has been determined at 2.7 A resolution. This structure is consistent with the hydrolysis of l-arginine through a metal-activated hydroxide mechanism. Given that human arginase II appears to play a role in regulating l-arginine bioavailability to NO synthase in human penile corpus cavernosum smooth muscle, the inhibition of human arginase II is a potential new strategy for the treatment of erectile dysfunction [Kim, N. N., Cox, J. D., Baggio, R. F., Emig, F. A., Mistry, S., Harper, S. L., Speicher, D. W., Morris, S. M., Ash, D. E., Traish, A. M., and Christianson, D. W. (2001) Biochemistry 40, 2678-2688]. Since NO synthase is found in human clitoral corpus cavernosum and vagina, we hypothesized that human arginase II is similarly present in these tissues and functions to regulate l-arginine bioavailability to NO synthase. Accordingly, hemodynamic studies conducted with a boronic acid arginase inhibitor in vivo are summarized, suggesting that the extrahepatic arginase plays a role in both male and female sexual arousal. Therefore, arginase II is a potential target for the treatment of male and female sexual arousal disorders.


  • Organizational Affiliation: 
    • Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Macromolecule Content 

  • Total Structure Weight: 202.93 kDa 
  • Atom Count: 14,599 
  • Modeled Residue Count: 1,836 
  • Deposited Residue Count: 1,836 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase II, mitochondrial precursor
A, B, C, D, E
A, B, C, D, E, F
306Homo sapiensMutation(s): 0 
Gene Names: ARG2
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78540 (Homo sapiens)
Explore P78540 
Go to UniProtKB:  P78540
PHAROS:  P78540
GTEx:  ENSG00000081181 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78540
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S2C

Query on S2C



Download:Ideal Coordinates CCD File
FA [auth D]
JA [auth E]
N [auth A]
R [auth B]
RA [auth F]
FA [auth D],
JA [auth E],
N [auth A],
R [auth B],
RA [auth F],
X [auth C]
S-2-(BORONOETHYL)-L-CYSTEINE
C5 H13 B N O5 S
XLVRIIJULVQAMP-BYPYZUCNSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
KA [auth F],
LA [auth F],
MA [auth F],
NA [auth F],
O [auth B],
S [auth C],
T [auth C],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MN

Query on MN



Download:Ideal Coordinates CCD File
CA [auth D]
DA [auth D]
GA [auth E]
HA [auth E]
K [auth A]
CA [auth D],
DA [auth D],
GA [auth E],
HA [auth E],
K [auth A],
L [auth A],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
U [auth C],
V [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
EA [auth D],
IA [auth E],
M [auth A],
QA [auth F],
W [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.247 (Depositor) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.994α = 90
b = 142.994β = 90
c = 127.328γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations