Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures

Watt, W.; Tulinsky, A.; Swenson, Richard P.; Watenpaugh, Keith David

doi:10.1016/0022-2836(91)90884-9

Cited by 194 publications

(264 citation statements)

References 22 publications

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“…Only the hydrogen bonds with favorable geometry have been taken into account. Most of the interactions are similar to those in other flavodoxin structures (16,(35)(36)(37)(38)(39). The phosphate group establishes O NH hydrogen bonds to residues of the N terminus of helix 1 (Gln 11 -Thr 15 ), plus further contacts to O ␥ of Thr 15 .…”

Section: X-ray Structures Of the W57l And Y94f Holoflavodoxins-supporting

confidence: 64%

How FMN Binds to Anabaena Apoflavodoxin

Lostao

Daoudi

Irún

et al. 2003

Journal of Biological Chemistry

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The active form of many proteins is a non-covalent complex between a polypeptide (the apoprotein) and a cofactor. Most flavoproteins are in this category (1). Among them, flavodoxins have been widely used to quantitate the energetics of apoprotein-cofactor complexes (2-7) because they can be conveniently overexpressed, deprived from the FMN cofactor, and reconstituted. Studies carried out on several flavodoxins indicate that a large part of the binding energy derives from interactions of the phosphate moiety of FMN with hydrogen donors situated at the N terminus of the first ␣-helix (Fig.

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Section: X-ray Structures Of the W57l And Y94f Holoflavodoxins-supporting

confidence: 64%

How FMN Binds to Anabaena Apoflavodoxin

Lostao

Daoudi

Irún

et al. 2003

Journal of Biological Chemistry

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“…On the other hand, it is , M1 known that flavin can interact via ring stacking with arolatic residues such as tryptophans, tyrosines and phenylalanaes. In particular, the non-covalently bound flavin cofactor in :iavodoxins and in a Tyr98Trp mutant [29] are sandwiched beween the aromatic in position 98, roughly parallel to it, and "rp 6° about 45 ° from being parallel [30,31]. Investigations made on the mutant Phe3~Ala also supported he idea that Phe 31 plays a crucial role both in protein structure md function, since such mutation both dramatically destabilzed the protein and substantially reduced its RNase activity unpublished results).…”

Section: R Consonni Et Al/febs Letters 372 (1995) 135 139mentioning

confidence: 87%

¹H‐NMR and photo‐CIDNP spectroscopies show a possible role for Trp²³ and Phe³¹ in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus

Consonni¹,

Limiroli

Molinari

et al. 1995

FEBS Letters

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“…In all structures, in the ox state, only the hydrophobic edge of the flavin ring (C7/C8 methyl groups) is exposed to the solvent, whereas the rest of the flavin ring, including the active center N5, is inaccessible to solvent. The crystal structures of D. vulgaris (Watt et al, 1991) and C. beijerinckii (Smith et al, 1977), determined in all three oxidation states, shows a conformational change in the 57-62 loop of the protein upon reduction from the ox to sq state, flipping the peptide residue (Gly 57 in C. beijerinckii and Gly 61 in D. vulgaris) so that the carbonyl oxygen engages in a hydrogen bond with the reduced N5H of flavin. Smaller conformational changes are seen on further reduction from the sq to hq state.…”

Section: St Rao Et Aimentioning

confidence: 99%

Structure of the oxidized long‐chain flavodoxin from anabaena 7120 at 2 å resolution

et al. 1992

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The structure of the long-chain flavodoxin from the photosynthetic cyanobacterium Anabaena 7120 has been determined at 2 A resolution by the molecular replacement method using the atomic coordinates of the long-chain flavodoxin from Anacystis nidulans. The structure of a third long-chain flavodoxin from Chondrus crispus has recently been reported. Crystals of oxidized A . 7120 flavodoxin belong to the monoclinic space group P2, with a = 48.0, b = 32.0, c = 51.6A, and 0 = 92", and one molecule in the asymmetric unit. The 2 A intensity data were collected with oscillation films at the CHESS synchrotron source and processed to yield 9,795 independent intensities with Rmerg of 0.07. Of these, 8,493 reflections had I > 2a and were used in the analysis. The model obtained by molecular replacement was initially refined by simulated annealing using the XPLOR program. Repeated refitting into omit maps and several rounds of conjugate gradient refinement led to an R-value of 0.185 for a model containing atoms for protein residues 2-169, flavin mononucleotide (FMN), and 104 solvent molecules. The FMN shows many interactions with the protein with the isoalloxazine ring, ribityl sugar, and the 5'-phosphate. The flavin ring has its pyrimidine end buried into the protein, and the functional dimethyl benzene edge is accessible to solvent. The FMN interactions in all three long-chain structures are similar except for the 04' of the ribityl chain, which interacts with the hydroxyl group of Thr 88 side chain in A. 7120, while with a water molecule in the other two. The phosphate group interacts with the atoms of the 9-15 loop as well as with NE1 of Trp 57. The N5 atom of flavin interacts with the amide NH of Ile 59 in A . 7120, whereas in A . nidulans it interacts with the amide NH of Val 59 in a similar manner. In C. crispus flavodoxin, N5 forms a hydrogen bond with the side chain hydroxyl group of the equivalent Thr 58. The hydrogen bond distances to the backbone NH groups in the first two flavodoxins are 3.6 A and 3.5 A , respectively, whereas in the third flavodoxin the distance is 3.1 A , close to the normal value. Even though the hydrogen bond distances are long in the first two cases, still they might have significant energy because their microenvironment in the protein is not accessible to solvent. In all three long-chain flavodoxins, a water molecule bridges the ends of the inserted loop in the os strand and minimally perturbs its hydrogen bonding with p4. Many of the water molecules in these proteins interact with the flavin binding loops. The conserved &core of the three long-chain and two short-chain flavodoxins superpose with root mean square deviations ranging from 0.48 A to 0.97 A .

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Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures

Cited by 194 publications

References 22 publications

How FMN Binds to Anabaena Apoflavodoxin

How FMN Binds to Anabaena Apoflavodoxin

¹H‐NMR and photo‐CIDNP spectroscopies show a possible role for Trp²³ and Phe³¹ in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus

Structure of the oxidized long‐chain flavodoxin from anabaena 7120 at 2 å resolution

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Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures

Cited by 194 publications

References 22 publications

How FMN Binds to Anabaena Apoflavodoxin

How FMN Binds to Anabaena Apoflavodoxin

1H‐NMR and photo‐CIDNP spectroscopies show a possible role for Trp23 and Phe31 in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus

Structure of the oxidized long‐chain flavodoxin from anabaena 7120 at 2 å resolution

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¹H‐NMR and photo‐CIDNP spectroscopies show a possible role for Trp²³ and Phe³¹ in nucleic acid binding by P2 ribonuclease from the archaeon Sulfolobus solfataricus