3Q9B

Crystal Structure of APAH complexed with M344


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases .

Lombardi, P.M.Angell, H.D.Whittington, D.A.Flynn, E.F.Rajashankar, K.R.Christianson, D.W.

(2011) Biochemistry 50: 1808-1817

  • DOI: https://doi.org/10.1021/bi101859k
  • Primary Citation of Related Structures:  
    3Q9B, 3Q9C, 3Q9E, 3Q9F

  • PubMed Abstract: 

    Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18 Å long "L"-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.


  • Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylpolyamine amidohydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
341Mycoplana ramosaMutation(s): 0 
Gene Names: aphAaph
UniProt
Find proteins for Q48935 (Mycoplana ramosa)
Explore Q48935 
Go to UniProtKB:  Q48935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ48935
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B3N
Query on B3N

Download Ideal Coordinates CCD File 
AC [auth E]
FD [auth G]
FE [auth I]
FF [auth K]
KA [auth B]
AC [auth E],
FD [auth G],
FE [auth I],
FF [auth K],
KA [auth B],
LB [auth D],
QC [auth F],
QE [auth J],
SD [auth H],
SF [auth L],
VA [auth C],
W [auth A]
4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide
C16 H25 N3 O3
MXWDSZWTBOCWBK-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AB [auth D]
AD [auth G]
AE [auth I]
AF [auth K]
BA [auth B]
AB [auth D],
AD [auth G],
AE [auth I],
AF [auth K],
BA [auth B],
BB [auth D],
BD [auth G],
BE [auth I],
BF [auth K],
CA [auth B],
CB [auth D],
CD [auth G],
CE [auth I],
CF [auth K],
DA [auth B],
DB [auth D],
DD [auth G],
DE [auth I],
DF [auth K],
EA [auth B],
EB [auth D],
ED [auth G],
EE [auth I],
EF [auth K],
FA [auth B],
FB [auth D],
FC [auth F],
GA [auth B],
GB [auth D],
GC [auth F],
HA [auth B],
HB [auth D],
HC [auth F],
IA [auth B],
IB [auth D],
IC [auth F],
JA [auth B],
JB [auth D],
JC [auth F],
JE [auth J],
KB [auth D],
KC [auth F],
KD [auth H],
KE [auth J],
KF [auth L],
LC [auth F],
LD [auth H],
LE [auth J],
LF [auth L],
M [auth A],
MC [auth F],
MD [auth H],
ME [auth J],
MF [auth L],
N [auth A],
NC [auth F],
ND [auth H],
NE [auth J],
NF [auth L],
O [auth A],
OC [auth F],
OD [auth H],
OE [auth J],
OF [auth L],
P [auth A],
PA [auth C],
PC [auth F],
PD [auth H],
PE [auth J],
PF [auth L],
Q [auth A],
QA [auth C],
QB [auth E],
QD [auth H],
QF [auth L],
R [auth A],
RA [auth C],
RB [auth E],
RD [auth H],
RF [auth L],
S [auth A],
SA [auth C],
SB [auth E],
T [auth A],
TA [auth C],
TB [auth E],
U [auth A],
UA [auth C],
UB [auth E],
V [auth A],
VB [auth E],
VC [auth G],
VE [auth K],
WB [auth E],
WC [auth G],
WE [auth K],
XB [auth E],
XC [auth G],
XD [auth I],
XE [auth K],
YB [auth E],
YC [auth G],
YD [auth I],
YE [auth K],
ZB [auth E],
ZC [auth G],
ZD [auth I],
ZE [auth K]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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DC [auth E]
ID [auth G]
IE [auth I]
IF [auth K]
NA [auth B]
DC [auth E],
ID [auth G],
IE [auth I],
IF [auth K],
NA [auth B],
OB [auth D],
TC [auth F],
TE [auth J],
VD [auth H],
VF [auth L],
YA [auth C],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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AA [auth A]
BC [auth E]
EC [auth E]
GD [auth G]
GE [auth I]
AA [auth A],
BC [auth E],
EC [auth E],
GD [auth G],
GE [auth I],
GF [auth K],
JD [auth G],
JF [auth K],
LA [auth B],
MB [auth D],
OA [auth B],
PB [auth D],
RC [auth F],
RE [auth J],
TD [auth H],
TF [auth L],
UC [auth F],
UE [auth J],
WA [auth C],
WD [auth H],
WF [auth L],
X [auth A],
ZA [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA
Query on NA

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CC [auth E]
HD [auth G]
HE [auth I]
HF [auth K]
MA [auth B]
CC [auth E],
HD [auth G],
HE [auth I],
HF [auth K],
MA [auth B],
NB [auth D],
SC [auth F],
SE [auth J],
UD [auth H],
UF [auth L],
XA [auth C],
Y [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.657α = 98.09
b = 119.734β = 95.15
c = 119.526γ = 115.33
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
APS-24IDCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description