2a4x

X-ray diffraction
1.4Å resolution

Crystal Structure Of Mitomycin C-Binding Protein Complexed with Metal-Free Bleomycin A2

Released:

Function and Biology Details

Reactions catalysed:
Hydrolysis of proteins in presence of ATP.
ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
Diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
ATP + kanamycin = ADP + kanamycin 3'-phosphate
IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate
D-glucose 6-phosphate = D-fructose 6-phosphate
Release of an N-terminal pyroglutamyl group from a polypeptide, the second amino acid generally not being Pro.
dUTP + H(2)O = dUMP + diphosphate
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
1-(5-phospho-beta-D-ribosyl)-ATP + diphosphate = ATP + 5-phospho-alpha-D-ribose 1-diphosphate
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
Random hydrolysis of (1->4)-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate
RH + Cl(-) + H(2)O(2) = RCl + 2 H(2)O
Hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans
Endonucleolytic cleavage of RNA, removing 21 and 42 nucleotides, respectively, from the 5'- and 3'-termini of a 5S-rRNA precursor.
UDP-N-acetyl-alpha-D-glucosamine + H(2)O = N-acetyl-D-mannosamine + UDP
(9Z)-(13S)-12,13-epoxyoctadeca-9,11,15-trienoate = (15Z)-12-oxophyto-10,15-dienoate
4-O-(beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + H(2)O = 4-O-(beta-L-arabinofuranosyl)-(2S,4S)-4-hydroxyproline + beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose
(S)-3-hydroxybutanoyl-CoA + NADP(+) = 3-acetoacetyl-CoA + NADPH
S-adenosyl-L-methionine + adenine in DNA = S-adenosyl-L-homocysteine + N-6-methyladenine in DNA 
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Chloride + O(2) = chlorite
ATP-dependent breakage, passage and rejoining of double-stranded DNA
ATP = 3',5'-cyclic AMP + diphosphate
A pyrimidine 5'-nucleotide + H(2)O = D-ribose 5-phosphate + a pyrimidine base
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.
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + UDP-N-acetyl-alpha-D-glucosamine = an [acyl-carrier-protein] + a UDP-3-O-(3-hydroxyacylyl)-N-acetyl-alpha-D-glucosamine
ATP + L-methionine + H(2)O = phosphate + diphosphate + S-adenosyl-L-methionine
A phosphate monoester + H(2)O = an alcohol + phosphate
A 4-O-methyl-D-glucopyranuronate ester + H(2)O = 4-O-methyl-D-glucuronic acid + an alcohol
2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H(2)O = ribonucleoside diphosphate + thioredoxin
D-allothreonine = glycine + acetaldehyde
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.
Diphosphate + H(2)O = 2 phosphate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
CoB + CoM + methanophenazine = CoM-S-S-CoB + dihydromethanophenazine
(1a) L-glutamine + H(2)O = L-glutamate + NH(3)
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
An aliphatic amide = a nitrile + H(2)O
6-phospho-beta-D-glucosyl-(1,4)-D-glucose + H(2)O = D-glucose + D-glucose 6-phosphate
L-asparagine + H(2)O = L-aspartate + NH(3)
2 superoxide + 2 H(+) = O(2) + H(2)O(2)
Urea + H(2)O = CO(2) + 2 NH(3)
L-serine + L-homocysteine = L-cystathionine + H(2)O
Xyloglucan + H(2)O = xyloglucan oligosaccharides
A carboxylic ester + H(2)O = an alcohol + a carboxylate
L-alanine = D-alanine
L-glutamate = D-glutamate
ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate
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.
Trypanothione + NADP(+) = trypanothione disulfide + NADPH
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO(3)(-) = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
ATP + phenylacetate + CoA = AMP + diphosphate + phenylacetyl-CoA
FAD + [protein]-L-threonine = [protein]-FMN-L-threonine + AMP
Random endo-hydrolysis of N-acetyl-beta-D-glucosaminide (1->4)-beta-linkages in chitin and chitodextrins
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
Thioredoxin + ROOH = thioredoxin disulfide + H(2)O + ROH
Nitric oxide + H(2)O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H(+)
An acyl-[acyl-carrier protein] + NADP(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADPH
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
Sucrose + ((1->6)-alpha-D-glucosyl)(n) = D-fructose + ((1->6)-alpha-D-glucosyl)(n+1)
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Orotidine 5'-phosphate = UMP + CO(2)
(2S)-flavan-4-ol + NADP(+) = (2S)-flavanone + NADPH
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
S-methyl-5'-thioadenosine + H(2)O = 5-(methylsulfanyl)-D-ribose + adenine
Prephenate = phenylpyruvate + H(2)O + CO(2)
NTP + H(2)O = NDP + phosphate
4 benzenediol + O(2) = 4 benzosemiquinone + 2 H(2)O
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
S-adenosyl-L-methionine + guanine(37) in tRNA = S-adenosyl-L-homocysteine + N(1)-methylguanine(37) in tRNA
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
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.
An aryl sulfate + a phenol = a phenol + an aryl sulfate
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
ATP + (R)-5-diphosphomevalonate = ADP + phosphate + isopentenyl diphosphate + CO(2)
A beta-lactam + H(2)O = a substituted beta-amino acid
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate
5,6-dihydrouracil + H(2)O = 3-ureidopropanoate
2 3-phospho-D-glycerate + 2 H(+) = D-ribulose 1,5-bisphosphate + CO(2) + H(2)O
Endohydrolysis of the N-glycosidic bond at one specific adenosine on the 28S rRNA.
Transfers a segment of a (1->4)-alpha-D-glucan to a new position in an acceptor, which may be glucose or a (1->4)-alpha-D-glucan
2 reduced ferredoxin + NADP(+) + H(+) = 2 oxidized ferredoxin + NADPH
N-acetyl-D-glucosamine 6-phosphate + H(2)O = D-glucosamine 6-phosphate + acetate
Hydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive maltose units from the non-reducing ends of the chains
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate = (S)-allantoin + CO(2)
D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H(2)O
D-glyceraldehyde 3-phosphate = glycerone phosphate
D-ribose 5-phosphate = D-ribulose 5-phosphate
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
D-xylopyranose = D-xylulose
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).
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.
ATP + pantetheine 4'-phosphate = diphosphate + 3'-dephospho-CoA
A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L) + 2 H(+)
A (Z)-hexadec-9-enoyl-[acyl-carrier protein] + a malonyl-[acyl-carrier protein] = a (Z)-3-oxooctadec-11-enoyl-[acyl-carrier protein] + CO(2) + an [acyl-carrier protein]
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-.
Cleavage of peptide bonds with very broad specificity.
(1a) S-adenosyl-L-methionine + precorrin-6B = S-adenosyl-L-homocysteine + precorrin-7 + CO(2)
Maltose = alpha,alpha-trehalose
4-maleylacetoacetate = 4-fumarylacetoacetate
Peptidylproline (omega=180) = peptidylproline (omega=0)
S-adenosyl-L-methionine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(ribonucleotide)-[mRNA] = S-adenosyl-L-homocysteine + a 5'-(N(7)-methyl 5'-triphosphoguanosine)-(2'-O-methyl-ribonucleotide)-[mRNA]
Endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans
(2E,6E)-farnesyl diphosphate + isopentenyl diphosphate = diphosphate + geranylgeranyl diphosphate
(R)-3-hydroxybutanoate + NAD(+) = acetoacetate + NADH
Endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
(S)-malate + NAD(+) = oxaloacetate + NADH
Random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
N,N-dimethylformamide + H(2)O = dimethylamine + formate
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanine + D-glutamate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate
S-(hydroxymethyl)glutathione + NAD(P)(+) = S-formylglutathione + NAD(P)H
GTP + IMP + L-aspartate = GDP + phosphate + N(6)-(1,2-dicarboxyethyl)-AMP
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
1D-chiro-inositol + NAD(+) = 2D-2,3,5/4,6-pentahydroxycyclohexanone + NADH
S-methyl-5'-thioadenosine + phosphate = adenine + S-methyl-5-thio-alpha-D-ribose 1-phosphate
S-adenosyl-L-homocysteine + H(2)O = L-homocysteine + adenosine
2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
L-threonine = glycine + acetaldehyde
Geranylgeranyl diphosphate = (+)-copalyl diphosphate
Beta-nicotinate D-ribonucleotide + 5,6-dimethylbenzimidazole = nicotinate + alpha-ribazole 5'-phosphate
(R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH
Hydrolysis of proteins and small molecule substrates at -Asn-|-Xaa- bonds.
Cleaves proteins of the adenovirus and its host cell at two consensus sites: -Yaa-Xaa-Gly-Gly-|-Xaa- and -Yaa-Xaa-Gly-Xaa-|-Gly- (in which Yaa is Met, Ile or Leu, and Xaa is any amino acid).
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH
Anthranilate + N,N-dimethyl-1,4-phenylenediamine + 2 NAD(+) = 2-(4-dimethylaminophenyl)diazenylbenzoate + 2 NADH
7-alpha,12-alpha-dihydroxy-3-oxochol-4-en-24-oyl-CoA = 12-alpha-hydroxy-3-oxochola-4,6-dien-24-oyl-CoA + H(2)O
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
L-carnitine + NAD(P)H + O(2) = (3R)-3-hydroxy-4-oxobutanoate + trimethylamine + NAD(P)(+) + H(2)O
Reduced plastocyanin + oxidized ferredoxin + light = oxidized plastocyanin + reduced ferredoxin
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
Hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
Methyl-CoM + CoB = CoM-S-S-CoB + methane
4-amino-5-aminomethyl-2-methylpyrimidine + H(2)O = 4-amino-5-hydroxymethyl-2-methylpyrimidine + ammonia
L-histidinol + H(2)O + 2 NAD(+) = L-histidine + 2 NADH
A (3R)-3-hydroxyacyl-[acyl-carrier-protein] + a UDP-3-O-((3R)-hydroxyacyl)-alpha-D-glucosamine = a UDP-2-N,3-O-bis((3R)-3-hydroxyacyl)-alpha-D-glucosamine + a holo-[acyl-carrier-protein]
5-hydroxyisourate + H(2)O = 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate
Beta-D-ribopyranose = beta-D-ribofuranose
ATP + glycerol = ADP + sn-glycerol 3-phosphate
(+)-trans-carveol + NAD(+) = (+)-(S)-carvone + NADH
Succinate + a quinone = fumarate + a quinol
Betaine aldehyde + NAD(+) + H(2)O = betaine + NADH
An aldehyde + NAD(P)(+) + H(2)O = a carboxylate + NAD(P)H
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine
Phenylacetaldehyde + NAD(+) + H(2)O = phenylacetate + NADH
D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H(2)O
Myo-inositol + NAD(+) = 2,4,6/3,5-pentahydroxycyclohexanone + NADH
3-dehydroquinate = 3-dehydroshikimate + H(2)O
Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H(2)O
ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu)
(3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H(2)O
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
5'-deoxyadenosine + H(2)O = 5-deoxy-D-ribose + adenine
Hydrolysis of terminal, non-reducing (1->4)-linked alpha-D-glucose residues with release of alpha-D-glucose
Hydrolysis of terminal, non-reducing beta-D-glucosyl residues with release of beta-D-glucose
Hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides
4-trimethylammoniobutanoate + 2-oxoglutarate + O(2) = 3-hydroxy-4-trimethylammoniobutanoate + succinate + CO(2) 
O-phospho-L-homoserine + H(2)O = L-threonine + phosphate
Acetyl-CoA + malonyl-[acyl-carrier-protein] = acetoacetyl-[acyl-carrier-protein] + CoA + CO(2) 
ATP + H(2)O = ADP + phosphate
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate
4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O
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
Inosine 5'-phosphate + NAD(+) + H(2)O = xanthosine 5'-phosphate + NADH
UDP-alpha-D-glucose = UDP-alpha-D-galactose
(R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H(2)O
Arachidonate + O(2) = (5Z,8Z,11Z,13E)-(15S)-15-hydroperoxyicosa-5,8,11,13-tetraenoate
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
D-ribulose 5-phosphate = D-xylulose 5-phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
VOC domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 138 amino acids
Theoretical weight: 15.47 KDa
Source organism: Streptomyces caespitosus
Expression system: Escherichia coli
UniProt:
  • Canonical: O05205 (Residues: 1-130; Coverage: 100%)
Gene name: mrd
Sequence domains: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
Structure domains: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P212121
Unit cell:
a: 47.248Å b: 52.405Å c: 107.862Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.222 0.264
Expression system: Escherichia coli