1NUS

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE COMPLEXED WITH ATP ANALOG AND NMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

STRUCTURAL CHARACTERIZATION OF A HUMAN CYTOSOLIC NMN/NaMN ADENYLYLTRANSFERASE AND IMPLICATION IN HUMAN NAD BIOSYNTHESIS

ZHANG, X.KURNASOV, O.V.KARTHIKEYAN, S.GRISHIN, N.V.OSTERMAN, A.L.ZHANG, H.

(2003) J Biol Chem 278: 13503-13511

  • DOI: https://doi.org/10.1074/jbc.M300073200
  • Primary Citation of Related Structures:  
    1NUP, 1NUQ, 1NUR, 1NUS, 1NUT, 1NUU

  • PubMed Abstract: 

    Pyridine dinucleotides (NAD and NADP) are ubiquitous cofactors involved in hundreds of redox reactions essential for the energy transduction and metabolism in all living cells. In addition, NAD also serves as a substrate for ADP-ribosylation of a number of nuclear proteins, for silent information regulator 2 (Sir2)-like histone deacetylase that is involved in gene silencing regulation, and for cyclic ADP ribose (cADPR)-dependent Ca(2+) signaling. Pyridine nucleotide adenylyltransferase (PNAT) is an indispensable central enzyme in the NAD biosynthesis pathways catalyzing the condensation of pyridine mononucleotide (NMN or NaMN) with the AMP moiety of ATP to form NAD (or NaAD). Here we report the identification and structural characterization of a novel human PNAT (hsPNAT-3) that is located in the cytoplasm and mitochondria. Its subcellular localization and tissue distribution are distinct from the previously identified human nuclear PNAT-1 and PNAT-2. Detailed structural analysis of PNAT-3 in its apo form and in complex with its substrate(s) or product revealed the catalytic mechanism of the enzyme. The characterization of the cytosolic human PNAT-3 provided compelling evidence that the final steps of NAD biosynthesis pathways may exist in mammalian cytoplasm and mitochondria, potentially contributing to their NAD/NADP pool.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. zhang@chop.swmed.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FKSG76
A, B
252Homo sapiensMutation(s): 0 
Gene Names: FKSG76
EC: 2.7.7.18 (UniProt), 2.7.7.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T66 (Homo sapiens)
Explore Q96T66 
Go to UniProtKB:  Q96T66
PHAROS:  Q96T66
GTEx:  ENSG00000163864 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96T66
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
NMN
Query on NMN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
C11 H16 N2 O8 P
DAYLJWODMCOQEW-TURQNECASA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.036α = 90
b = 79.036β = 90
c = 145.987γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description