9NTH | pdb_00009nth

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin monophosphate (PMP)

  • Classification: HYDROLASE
  • Organism(s): Helix pomatia
  • Expression System: Komagataella pastoris
  • Mutation(s): No 

  • Deposited: 2025-03-18 Released: 2025-06-18 
  • Deposition Author(s): Kaur, G., Horton, J.R., Cheng, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.199 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for the substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase.

Kaur, G., Horton, J.R., Tzertzinis, G., Zhou, J., Schildkraut, I., Cheng, X.

(2025) J Biological Chem : 110357-110357

  • DOI: https://doi.org/10.1016/j.jbc.2025.110357
  • Primary Citation of Related Structures:  
    9NTE, 9NTF, 9NTH, 9NTI, 9NTJ, 9NTK

  • PubMed Abstract: 

    Helix pomatia AMP deaminase (HPAMPD), an enzyme enriched in the foot muscle of the mollusk Helix pomatia, exhibits deaminase activity on adenosine-5'-monophosphate (AMP). HPAMPD is the first member of the adenosine deaminase-related growth factor (ADGF) family to prefer the nucleotideAMP over the nucleoside adenosine. To investigate the substrate selectivity of HPAMPD, we determined its structure in both the apo form and in complex with the adenosine analogs pentostatin and pentostatin-5'-monophosphate. Structurally, HPAMPD adopts a fold similar to human ADA2, an ADGF family member. HPAMPD has acquired the ability to interact with the 5'-monophosphate group of AMP through polar and charged residues located in three key structural elements: (1) the loop immediately following strand β1; (2) the loop between helices αH and αI; and (3) the end of strand β5 and its adjacent loop. We engineered a chimeric deaminase by integrating these elements from HPAMPD into another related mollusk nucleoside adenosine deaminase, Aplysia ADGF. The chimeric enzyme efficiently deaminates AMP, demonstrating a gained substrate specificity, while retaining the adenosine deamination activity of Aplysia ADGF. The phosphate-binding feature of HPAMPD is a hallmark of nucleotide deaminases, conserved among AMP and N6-methyl-AMP (6mAMP) deaminases. We discuss the human adenosine deaminases each with distinct substrate specificities for the nucleoside, the nucleotide (AMP), and its methylated form, 6mAMP.

    • Organizational Affiliation: 

    Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMP Deaminase
A, B, C, D
541Helix pomatiaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CDW (Subject of Investigation/LOI)
Query on A1CDW
Download Ideal Coordinates CCD File 
IE [auth D],
KD [auth C],
MA [auth A],
WB [auth B]		pentostatin 5'-phosphate
C11 H17 N4 O7 P
NZYBWACXTRESTQ-JQCXWYLXSA-N
NAG
Query on NAG
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AC [auth C]
J [auth A]
K [auth A]
L [auth A]
LD [auth D]
AC [auth C],
J [auth A],
K [auth A],
L [auth A],
LD [auth D],
MD [auth D],
ND [auth D],
OA [auth B],
PA [auth B],
QA [auth B],
ZB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BTB
Query on BTB
Download Ideal Coordinates CCD File 
O [auth A],
WA [auth B]		2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
PEG
Query on PEG
Download Ideal Coordinates CCD File 
HD [auth C]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File 
FA [auth A]
FE [auth D]
KA [auth A]
MB [auth B]
TC [auth C]
FA [auth A],
FE [auth D],
KA [auth A],
MB [auth B],
TC [auth C],
UC [auth C],
YB [auth C],
ZD [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
HE [auth D],
JD [auth C],
LA [auth A],
VB [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AD [auth C]
AE [auth D]
BA [auth A]
AA [auth A],
AB [auth B],
AD [auth C],
AE [auth D],
BA [auth A],
BB [auth B],
BC [auth C],
BD [auth C],
BE [auth D],
CA [auth A],
CB [auth B],
CC [auth C],
CD [auth C],
CE [auth D],
DA [auth A],
DB [auth B],
DC [auth C],
DD [auth C],
DE [auth D],
EA [auth A],
EB [auth B],
EC [auth C],
ED [auth C],
EE [auth D],
FB [auth B],
FC [auth C],
FD [auth C],
GA [auth A],
GB [auth B],
GC [auth C],
GD [auth C],
GE [auth D],
HA [auth A],
HB [auth B],
HC [auth C],
I [auth A],
IA [auth A],
IB [auth B],
IC [auth C],
ID [auth C],
JA [auth A],
JB [auth B],
JC [auth C],
KB [auth B],
KC [auth C],
LB [auth B],
LC [auth C],
M [auth A],
MC [auth C],
N [auth A],
NA [auth B],
NB [auth B],
NC [auth C],
OB [auth B],
OC [auth C],
OD [auth D],
P [auth A],
PB [auth B],
PC [auth C],
PD [auth D],
Q [auth A],
QB [auth B],
QC [auth C],
QD [auth D],
R [auth A],
RA [auth B],
RB [auth B],
RC [auth C],
RD [auth D],
S [auth A],
SA [auth B],
SB [auth B],
SC [auth C],
SD [auth D],
T [auth A],
TA [auth B],
TB [auth B],
TD [auth D],
U [auth A],
UA [auth B],
UB [auth B],
UD [auth D],
V [auth A],
VA [auth B],
VC [auth C],
VD [auth D],
W [auth A],
WC [auth C],
WD [auth D],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth C],
XD [auth D],
Y [auth A],
YA [auth B],
YC [auth C],
YD [auth D],
Z [auth A],
ZA [auth B],
ZC [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.199 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.992α = 90
b = 81.936β = 92.134
c = 212.195γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM134744
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR160029

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Database references