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CRYSTAL STRUCTURE OF THE HETERODIMERIC NITRATE REDUCTASE FROM RHODOBACTER SPHAEROIDES

The structure was published by Arnoux, P., Sabaty, M., Alric, J., et al., Guigliarelli, B., Adriano, J.-M., and Pignol, D., in 2003 in a paper entitled "Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 3.2 Å and deposited in 2003.

The experimental data on which the structure is based was also deposited.

This PDB entry contains a complex of 2 biomacromolecules, namely PERIPLASMIC NITRATE REDUCTASE and DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
C PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
E PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
G PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
I PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
K PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
M PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
O PERIPLASMIC NITRATE REDUCTASE Q53176 (30-831) (NAPA_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 802 98%
B DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
D DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
F DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
H DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
J DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
L DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
N DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%
P DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Q53177 (25-154) (NAPB_RHOS4)search Rhodobacter sphaeroides 2.4.1search 100% 130 97%


This entry contains 2 unique UniProt proteins:

UniProt accession Name Organism PDB
Q53176 (30 - 831) PERIPLASMIC NITRATE REDUCTASE Rhodobacter sphaeroides
Q53177 (25 - 154) DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE Rhodobacter sphaeroides

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A, C, E, G, I, K, M, O (Q53176) Formate dehydrogenase/DMSO reductase, C-terminal domainsearch, Formate dehydrogenase/DMSO reductase, domains 1-3search Rossmann foldsearch, Dimethylsulfoxide Reductase, domain 2search, Barwin-like endoglucanasessearch PF00384: Molybdopterin oxidoreductasesearch, PF01568: Molydopterin dinucleotide binding domainsearch, PF04879: Molybdopterin oxidoreductase Fe4S4 domainsearch
B, D, F, H, J, L, N, P (Q53177) Di-heme elbow motifsearch PF03892: Nitrate reductase cytochrome c-type subunit (NapB)search

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A, C, E, G, I, K, M, O (Q53176) molybdenum ion bindingsearch nitrate reductase activitysearch oxidoreductase activitysearch 4 iron, 4 sulfur cluster bindingsearch metal ion bindingsearch iron-sulfur cluster bindingsearch electron carrier activitysearch iron ion bindingsearch oxidation-reduction processsearch nitrate assimilationsearch Mo-molybdopterin cofactor biosynthetic processsearch periplasmic spacesearch
B, D, F, H, J, L, N, P (Q53177) metal ion bindingsearch oxidation-reduction processsearch periplasmic spacesearch

Chain InterPro annotation
A, C, E, G, I, K, M, O Molybdopterin oxidoreductasesearch Molydopterin dinucleotide-binding domainsearch Molybdopterin oxidoreductase, 4Fe-4S domainsearch Aspartate decarboxylase-like domainsearch Periplasmic nitrate reductase, large subunitsearch Molybdopterin oxidoreductase, molybdopterin cofactor binding sitesearch
B, D, F, H, J, L, N, P Nitrate reductase cytochrome c-type subunit NapBsearch Multihaem cytochromesearch Periplasmic nitrate reductase NapB subunit, heme binding domainsearch