1jy3

X-ray diffraction
1.6Å resolution

Crystal Structure of the Central Region of Bovine Fibrinogen (E5 Fragment) at 1.4 Angstroms Resolution

Released:
Source organism: Bos taurus

Function and Biology Details

Reactions catalysed:
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)(+) + H(2)O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val
[Protein]-N(pi)-phospho-L-histidine + lactose(Side 1) = [protein]-L-histidine + lactose 6'-phosphate(Side 2)
ATP + a protein = ADP + a phosphoprotein
RH + [reduced NADPH--hemoprotein reductase] + O(2) = ROH + [oxidized NADPH--hemoprotein reductase] + H(2)O
Release of N-terminal proline from a peptide.
Release of an N-terminal amino acid, Xaa-|-Yaa-, in which Xaa is preferably Leu, but may be other amino acids including Pro although not Arg or Lys, and Yaa may be Pro. Amino acid amides and methyl esters are also readily hydrolyzed, but rates on arylamides are exceedingly low.
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H(2)O
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
Cleavage of peptide bonds with very broad specificity.
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
S-adenosyl-L-methionine + a catechol = S-adenosyl-L-homocysteine + a guaiacol
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
2 glutathione + ROOH = glutathione disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
ATP + RNA(n) = diphosphate + RNA(n+1)
TSAVLQ-|-SGFRK-NH(2) and SGVTFQ-|-GKFKK the two peptides corresponding to the two self-cleavage sites of the SARS 3C-like proteinase are the two most reactive peptide substrates. The enzyme exhibits a strong preference for substrates containing Gln at P1 position and Leu at P2 position.
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
[Amino group carrier protein]-C-terminal-gamma-(L-lysyl)-L-glutamate + H(2)O = [amino group carrier protein]-C-terminal-L-glutamate + L-lysine
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
(S)-dihydroorotate + fumarate = orotate + succinate
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
(Polyphosphate)(n) + H(2)O = (polyphosphate)(n-1) + phosphate
L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
(1a) ATP + [DNA ligase]-L-lysine = [DNA ligase]-N(6)-(5'-adenylyl)-L-lysine + diphosphate
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
A beta-lactam + H(2)O = a substituted beta-amino acid
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
S-adenosyl 3-(methylthio)propylamine + putrescine = 5'-S-methyl-5'-thioadenosine + spermidine
Cleaves -Ala-|-Ser- and -Ala-|-Ala- bonds in the scaffold protein.
Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
Hydrolyzes glutaminyl bonds, and activity is further restricted by preferences for the amino acids in P6 - P1' that vary with the species of potyvirus, e.g. Glu-Xaa-Xaa-Tyr-Xaa-Gln-|-(Ser or Gly) for the enzyme from tobacco etch virus. The natural substrate is the viral polyprotein, but other proteins and oligopeptides containing the appropriate consensus sequence are also cleaved.
Hydrolyzes a Gly-|-Gly bond at its own C-terminus, commonly in the sequence -Tyr-Xaa-Val-Gly-|-Gly, in the processing of the potyviral polyprotein.
Cutin + H(2)O = cutin monomers
Maltose = alpha,alpha-trehalose
2 H(2)O(2) = O(2) + 2 H(2)O
2 phenolic donor + H(2)O(2) = 2 phenoxyl radical of the donor + 2 H(2)O
An aldehyde + H(2)O + 2 oxidized ferredoxin = a carboxylate + 2 H(+) + 2 reduced ferredoxin
[F-actin]-L-methionine + NADPH + O(2) + H(+) = [F-actin]-L-methionine-(R)-S-oxide + NADP(+) + H(2)O
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
(S)-malate = fumarate + H(2)O
ADP-alpha-D-glucose + D-glucose 6-phosphate = ADP + alpha,alpha-trehalose 6-phosphate
Eliminative cleavage of alginate to give oligosaccharides with 4-deoxy-alpha-L-erythro-hex-4-enuronosyl groups at their non-reducing ends and beta-D-mannuronate at their reducing end.
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
L-arginine + 2-oxoglutarate + O(2) = (3S)-3-hydroxy-L-arginine + succinate + CO(2)
D-firefly luciferin + O(2) + ATP = firefly oxyluciferin + CO(2) + AMP + diphosphate + light
Acetyl-CoA + a 2-deoxystreptamine antibiotic = CoA + N(3)-acetyl-2-deoxystreptamine antibiotic
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
ATP + protein L-histidine = ADP + protein N-phospho-L-histidine
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(27) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(27)
ATP + thiamine = AMP + thiamine diphosphate
Hydrolysis of the -Gly-|-Gly- bond in the pentaglycine inter-peptide link joining staphylococcal cell wall peptidoglycans.
Beta-D-ribopyranose = beta-D-ribofuranose
NAD(+) + protein-L-arginine = nicotinamide + N(omega)-(ADP-D-ribosyl)-protein-L-arginine
2 nitric oxide + 2 O(2) + NAD(P)H = 2 nitrate + NAD(P)(+) + H(+)
GDP-beta-L-fucose + NADP(+) = GDP-4-dehydro-alpha-D-rhamnose + NADPH
Malonyl-CoA + an [acyl-carrier-protein] = CoA + a malonyl-[acyl-carrier-protein]
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
Hg + NADP(+) + H(+) = Hg(2+) + NADPH
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
L-histidine-[translation elongation factor 2] + S-adenosyl-L-methionine = 2-((3S)-3-amino-3-carboxypropyl)-L-histidine-[translation elongation factor 2] + S-methyl-5'-thioadenosine
Glutarate + 2-oxoglutarate + O(2) = (S)-2-hydroxyglutarate + succinate + CO(2)
2 ATP = 2 diphosphate + cyclic di-3',5'-adenylate
Hydrolysis of terminal, non-reducing branched (1->3)-alpha-D-galactosidic residues, producing free D-galactose
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
Quercetin + O(2) = 2-(3,4-dihydroxybenzoyloxy)-4,6-dihydroxybenzoate + CO + H(+)
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
ATP + [biotin carboxyl-carrier protein]-biotin-N(6)-L-lysine + hydrogencarbonate- = ADP + phosphate + [biotin carboxyl-carrier protein]-carboxybiotin-N(6)-L-lysine
ATP + FMN = diphosphate + FAD
Autocatalytically cleaves itself from the polyprotein of the foot-and-mouth disease virus by hydrolysis of a Lys-|-Gly bond, but then cleaves host cell initiation factor eIF-4G at bonds -Gly-|-Arg- and -Lys-|-Arg-.
Choline = trimethylamine + acetaldehyde
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
L-histidinol phosphate + H(2)O = L-histidinol + phosphate
S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine(34) in tRNA(Leu) = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2'-O-methyluridine(34) in tRNA(Leu)
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
ATP + riboflavin = ADP + FMN
Preferential cleavage at the carboxyl of hydrophobic amino acids, but fails to cleave 15-Leu-|-Tyr-16, 16-Tyr-|-Leu-17 and 24-Phe-|-Phe-25 of insulin B chain. Activates trypsinogen, and degrades keratin.
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
NAD(P)H + a quinone = NAD(P)(+) + a hydroquinone
NAD(P)H + O(2) = NAD(P)(+) + H(2)O(2)
ATP + glycerol = ADP + sn-glycerol 3-phosphate
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
Random hydrolysis of (1->6)-alpha-D-mannosidic linkages in unbranched (1->6)-mannans
ATP + acetyl-CoA + HCO(3)(-) = ADP + phosphate + malonyl-CoA
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactolipids
Alpha-D-glucose = beta-D-glucose
Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate
dUTP + H(2)O = dUMP + diphosphate
5-phospho-beta-D-ribosylamine + diphosphate + L-glutamate = L-glutamine + 5-phospho-alpha-D-ribose 1-diphosphate + H(2)O
3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholanate + NAD(+) = 3-alpha,12-alpha-dihydroxy-7-oxo-5-beta-cholanate + NADH
6-phospho-D-glucono-1,5-lactone + H(2)O = 6-phospho-D-gluconate
ATP-dependent breakage, passage and rejoining of double-stranded DNA
(S)-ureidoglycolate = glyoxylate + urea
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Isochorismate + H(2)O = (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate
ATP-dependent cleavage of peptide bonds with broad specificity.
Carbamoyl phosphate + L-aspartate = phosphate + N-carbamoyl-L-aspartate
N(2)-acetyl-L-ornithine + L-glutamate = L-ornithine + N-acetyl-L-glutamate
Blasticidin S + H(2)O = deaminohydroxyblasticidin S + NH(3)
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Triacylglycerol + H(2)O = diacylglycerol + a carboxylate
Acyl-[acyl-carrier-protein] + malonyl-[acyl-carrier-protein] = 3-oxoacyl-[acyl-carrier-protein] + CO(2) + [acyl-carrier-protein]
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine
Isocitrate = succinate + glyoxylate
ATP = 3',5'-cyclic AMP + diphosphate
D-xylopyranose = D-xylulose
2-dehydro-3-deoxy-6-phosphate-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Preferential cleavage: Glu-|-, Asp-|-.
5-methyltetrahydrofolate + NAD(P)(+) = 5,10-methylenetetrahydrofolate + NAD(P)H
2 bilirubin + O(2) = 2 biliverdin + 2 H(2)O
(S)-3-hydroxyacyl-CoA + NAD(+) = 3-oxoacyl-CoA + NADH
ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
3-dehydroquinate = 3-dehydroshikimate + H(2)O
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
A primary alcohol + NAD(+) = an aldehyde + NADH
AMP + H(2)O = D-ribose 5-phosphate + adenine
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
A 2'-deoxyribonucleoside 5'-monophosphate + H(2)O = a 2'-deoxyribonucleoside + phosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
4-fumarylacetoacetate + H(2)O = acetoacetate + fumarate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fibrinogen alpha chain Chains: N, Q
Molecule details ›
Chains: N, Q
Length: 53 amino acids
Theoretical weight: 6.17 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P02672 (Residues: 48-100; Coverage: 9%)
Gene name: FGA
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Fibrinogen beta chain Chains: O, R
Molecule details ›
Chains: O, R
Length: 56 amino acids
Theoretical weight: 6.25 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P02676 (Residues: 61-116; Coverage: 12%)
Gene name: FGB
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Fibrinogen gamma-B chain Chains: P, S
Molecule details ›
Chains: P, S
Length: 48 amino acids
Theoretical weight: 5.48 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: P12799 (Residues: 25-72; Coverage: 11%)
Gene name: FGG
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X26C
Spacegroup: P212121
Unit cell:
a: 53.7Å b: 59.1Å c: 97.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.194 0.22