1wh1

Solution NMR

Solution structure of the fourth PDZ domain of KIAA1095 protein

Released:
Source organism: Homo sapiens
Entry authors: Qin X, Saito K, Kigawa T, Hayashi F, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reactions catalysed:
Succinyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-succinyldihydrolipoyl)lysine
RX + glutathione = HX + R-S-glutathione
5,10-methylenetetrahydrofolate + dUMP = dihydrofolate + dTMP
L-arginine + H(2)O = L-ornithine + urea
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
dUTP + H(2)O = dUMP + diphosphate
(1a) 2 cob(II)alamin + 2 [corrinoid adenosyltransferase] = 2 [corrinoid adenosyltransferase]-cob(II)alamin
UDP-glucose + (1,4-beta-D-glucosyl)(n) = UDP + (1,4-beta-D-glucosyl)(n+1)
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
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.
O-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate
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).
L-glutamate + H(2)O + NADP(+) = 2-oxoglutarate + NH(3) + NADPH
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.
Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
(8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate
ATP + 6-hydroxymethyl-7,8-dihydropterin = AMP + 6-hydroxymethyl-7,8-dihydropterin diphosphate
ATP + dTMP = ADP + dTDP
5,10-methylenetetrahydrofolate + glycine + H(2)O = tetrahydrofolate + L-serine
dCTP + 2 H(2)O = dUMP + diphosphate + NH(3)
ATP + a protein = ADP + a phosphoprotein
Endopeptidase with a preference for cleavage when the P1 position is occupied by Glu-|- and the P1' position is occupied by Gly-|-
3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMNH(2) + O(2) = 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione + FMN + H(2)O
ATP + glycerol = ADP + sn-glycerol 3-phosphate
Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH
N-(5-phospho-D-ribosyl)-anthranilate + diphosphate = anthranilate + 5-phospho-alpha-D-ribose 1-diphosphate
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Hydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose and cellotetraose, releasing cellobiose from the non-reducing ends of the chains
Release of N-terminal proline from a peptide.
A beta-lactam + H(2)O = a substituted beta-amino acid
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.
Succinate + a quinone = fumarate + a quinol
ATP + H(2)O + cellular protein(Side 1) = ADP + phosphate + cellular protein(Side 2)
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.
An aldehyde + NAD(+) + H(2)O = a carboxylate + NADH
An acyl-[acyl-carrier protein] + NAD(+) = a trans-2,3-dehydroacyl-[acyl-carrier protein] + NADH
ATP-dependent breakage, passage and rejoining of double-stranded DNA
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate = (3E)-2-oxohex-3-enedioate
An aldehyde + H(2)O + 2 oxidized ferredoxin = a carboxylate + 2 H(+) + 2 reduced ferredoxin
2 alpha,alpha'-trehalose 6-mycolate = alpha,alpha'-trehalose + alpha,alpha'-trehalose 6,6'-bismycolate
ATP + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminoheptanedioate
NTP + H(2)O = NDP + phosphate
Alpha-D-glucose 6-phosphate = beta-D-glucose 6-phosphate
7,8-dihydroneopterin 3'-triphosphate + H(2)O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
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.
dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
1-haloalkane + H(2)O = a primary alcohol + halide
N-carbamoylputrescine + H(2)O = putrescine + CO(2) + NH(3)
6-hydroxymethyl-7,8-dihydropterin diphosphate + 4-aminobenzoate = diphosphate + dihydropteroate
NAD(+) + H(2)O = ADP-D-ribose + nicotinamide
ATP + H(2)O + a folded polypeptide = ADP + phosphate + an unfolded polypeptide
Cleavage of peptide bonds with very broad specificity.
(+)-muconolactone = 5-oxo-4,5-dihydrofuran-2-acetate
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
Chorismate = prephenate
L-lysine + NADPH + O(2) = N(6)-hydroxy-L-lysine + NADP(+) + H(2)O
Peptidylproline (omega=180) = peptidylproline (omega=0)
An acylphosphate + H(2)O = a carboxylate + phosphate
ATP + H(2)O = ADP + phosphate
ATP + thymidine = ADP + thymidine 5'-phosphate
4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O
(3R)-3-hydroxyacyl-[acyl-carrier-protein] + NADP(+) = 3-oxoacyl-[acyl-carrier-protein] + NADPH
Aceneneuramate = N-acetyl-D-mannosamine + pyruvate
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
ATP + N-acetyl-L-glutamate = ADP + N-acetyl-L-glutamate 5-phosphate
ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate
ATP + (R)-5-phosphomevalonate = ADP + (R)-5-diphosphomevalonate
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
3-deoxy-D-manno-octulosonate 8-phosphate + H(2)O = 3-deoxy-D-manno-octulosonate + phosphate
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units
Acyl-CoA + 1,2-diacylglycerol = CoA + triacylglycerol
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E3 ubiquitin-protein ligase PDZRN3 Chain: A
Molecule details ›
Chain: A
Length: 124 amino acids
Theoretical weight: 13.86 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q9UPQ7 (Residues: 405-515; Coverage: 10%)
Gene names: KIAA1095, LNX3, PDZRN3, SEMCAP3
Sequence domains: PDZ domain
Structure domains: Pdz3 Domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Refinement method: torsion angle dynamic
Chemical shifts: BMR11201  
Expression system: Not provided