2NAP

DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS

• PDB DOI: https://doi.org/10.2210/pdb2NAP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Desulfovibrio desulfuricans
• Mutation(s): No 


• Deposited: 1998-09-18 Released: 1999-09-19 
• Deposition Author(s): Dias, J.M., Than, M., Humm, A., Huber, R., Bourenkov, G., Bartunik, H., Bursakov, S., Calvete, J., Caldeira, J., Carneiro, C., Moura, J., Moura, I., Romao, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.

Dias, J.M., Than, M.E., Humm, A., Huber, R., Bourenkov, G.P., Bartunik, H.D., Bursakov, S., Calvete, J., Caldeira, J., Carneiro, C., Moura, J.J., Moura, I., Romao, M.J.

(1999) Structure 7: 65-79

• PubMed: 10368307 
• DOI: https://doi.org/10.1016/s0969-2126(99)80010-0
• Primary Citation of Related Structures:  
  2NAP


• PubMed Abstract: 
  

  The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (MGD) cofactor and one [4Fe-4S] cluster in a single polypeptide chain of 723 amino acid residues. To date, there is no crystal structure of a nitrate reductase.

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Organizational Affiliation: 

Departamento de Quimica, CQFB, FCT, Universidade Nova de Lisboa, Caparica, Portugal.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.52 kDa 
• Atom Count: 6,301 
• Modelled Residue Count: 720 
• Deposited Residue Count: 723 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PERIPLASMIC NITRATE REDUCTASE)	A	723	Desulfovibrio desulfuricans	Mutation(s): 0
UniProt
Find proteins for P81186 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P81186  Go to UniProtKB:  P81186

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGD	D [auth A], E [auth A]	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE C20 H26 N10 O13 P2 S2 VQAGYJCYOLHZDH-ILXWUORBSA-N
SF4	B [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
MES	F [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MO	C [auth A]	MOLYBDENUM ATOM Mo ZOKXTWBITQBERF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.267 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.26	α = 90
b = 106.26	β = 90
c = 134.91	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
SHARP	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-09-19 
Deposition Author(s): Dias, J.M., Than, M., Humm, A., Huber, R., Bourenkov, G., Bartunik, H., Bursakov, S., Calvete, J., Caldeira, J., Carneiro, C., Moura, J., Moura, I., Romao, M.J.

Revision History  

• Version 1.0: 1999-09-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-02-06
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations