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Showing metabocard for 1-Pyrroline-2-carboxylic acid (HMDB0006875)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-08-13 17:53:39 UTC
Update Date2023-02-21 17:17:22 UTC
HMDB IDHMDB0006875
Secondary Accession Numbers
  • HMDB06875
Metabolite Identification
Common Name1-Pyrroline-2-carboxylic acid
Description1-Pyrroline-2-carboxylic acid, also known as delta1-pyrroline 2-carboxylate, belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms. 1-Pyrroline-2-carboxylic acid is a moderately basic compound (based on its pKa). 1-Pyrroline-2-carboxylic acid exists in all living organisms, ranging from bacteria to humans. 1-pyrroline-2-carboxylic acid can be biosynthesized from D-proline through its interaction with the enzyme D-amino-acid oxidase. The product resulting from formal oxidation of DL-proline by loss of hydrogen from the nitrogen and from the carbon alpha to the carboxylic acid, with the formation of a C=N bond. In humans, 1-pyrroline-2-carboxylic acid is involved in the metabolic disorder called hyperprolinemia type II.
Structure
Data?1676999842
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0006875 (1-Pyrroline-2-carboxylic acid)


  Mrv1652309152018192D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  1  8  1  0  0  0  0
M  END
Download

3D MOL for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HMDB0006875
     RDKit          3D
1-Pyrroline-2-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.4854   -1.8375    0.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0006   -0.7758    0.0164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8879    0.1635   -0.4847 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5615   -0.5197   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3554   -1.3317    0.4400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7543    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3338    0.7410    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0850    0.7115   -0.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8295    1.0951   -0.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3822   -1.0451    1.0527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.9494   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9918    1.0170    1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1261    1.3627   -0.0667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379    1.6100   -0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3420    0.5127   -1.6088 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  6 10  1  0
  6 11  1  0
  7 12  1  0
  7 13  1  0
  8 14  1  0
  8 15  1  0
M  END
Download

3D SDF for HMDB0006875 (1-Pyrroline-2-carboxylic acid)


  Mrv1652309152018192D          

  8  8  0  0  0  0            999 V2000
10000.682310000.1792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.3973 9999.7677    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.682310001.0035    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.297510000.2623    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.6301 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.8850 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.7100 9998.9927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9649 9999.7773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  1  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0006875

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1=NCCC1

> <INCHI_IDENTIFIER>
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)

> <INCHI_KEY>
RHTAIKJZSXNELN-UHFFFAOYSA-N

> <FORMULA>
C5H7NO2

> <MOLECULAR_WEIGHT>
113.1146

> <EXACT_MASS>
113.047678473

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.81138734712021

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydro-2H-pyrrol-1-ium-5-carboxylate

> <ALOGPS_LOGP>
0.25

> <JCHEM_LOGP>
0.5292144963333332

> <ALOGPS_LOGS>
-1.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9331828370415765

> <JCHEM_PKA_STRONGEST_BASIC>
1.7241099274971199

> <JCHEM_POLAR_SURFACE_AREA>
54.099999999999994

> <JCHEM_REFRACTIVITY>
49.890800000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dihydro-3H-pyrrol-1-ium-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HMDB0006875
     RDKit          3D
1-Pyrroline-2-carboxylic acid
 15 15  0  0  0  0  0  0  0  0999 V2000
    2.4854   -1.8375    0.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0006   -0.7758    0.0164 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8879    0.1635   -0.4847 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5615   -0.5197   -0.0036 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3554   -1.3317    0.4400 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6728   -0.7543    0.2613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3338    0.7410    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0850    0.7115   -0.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8295    1.0951   -0.0601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3822   -1.0451    1.0527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0135   -0.9494   -0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9918    1.0170    1.3529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1261    1.3627   -0.0667 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5379    1.6100   -0.4170 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3420    0.5127   -1.6088 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  4  1  0
  3  9  1  0
  6 10  1  0
  6 11  1  0
  7 12  1  0
  7 13  1  0
  8 14  1  0
  8 15  1  0
M  END
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PDB for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

HEADER    PROTEIN                                 15-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-SEP-20         0                                  
HETATM    1  C   UNK     0    8667.9408667.001   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8669.2758666.233   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8667.9408668.540   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0    8665.3558667.156   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0    8664.1108666.251   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8664.5858664.786   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8666.1258664.786   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8666.6018666.251   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    5    8                                                       
CONECT    5    6    4                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    4    1                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

COMPND    HMDB0006875
HETATM    1  O1  UNL     1       2.485  -1.838   0.479  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.001  -0.776   0.016  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.888   0.164  -0.485  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.561  -0.520  -0.004  1.00  0.00           C  
HETATM    5  N1  UNL     1      -0.355  -1.332   0.440  1.00  0.00           N  
HETATM    6  C3  UNL     1      -1.673  -0.754   0.261  1.00  0.00           C  
HETATM    7  C4  UNL     1      -1.334   0.741   0.329  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.085   0.712  -0.535  1.00  0.00           C  
HETATM    9  H1  UNL     1       2.829   1.095  -0.060  1.00  0.00           H  
HETATM   10  H2  UNL     1      -2.382  -1.045   1.053  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.013  -0.949  -0.756  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.992   1.017   1.353  1.00  0.00           H  
HETATM   13  H5  UNL     1      -2.126   1.363  -0.067  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.538   1.610  -0.417  1.00  0.00           H  
HETATM   15  H7  UNL     1      -0.342   0.513  -1.609  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    5    8
CONECT    5    6
CONECT    6    7   10   11
CONECT    7    8   12   13
CONECT    8   14   15
END
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SMILES for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

OC(=O)C1=NCCC1
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INCHI for HMDB0006875 (1-Pyrroline-2-carboxylic acid)

InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
1-Pyrroline-2-carboxylateChEBI
delta1-Pyrroline 2-carboxylateChEBI
1-Pyrroline 2-carboxylateKegg
delta1-Pyrroline 2-carboxylic acidGenerator
Δ1-pyrroline 2-carboxylateGenerator
Δ1-pyrroline 2-carboxylic acidGenerator
1-Pyrroline 2-carboxylic acidGenerator
3,4-Dihydro-2H-pyrrole-5-carboxylateHMDB
3,4-Dihydro-2H-pyrrole-5-carboxylic acidHMDB
D1-Pyrroline 2-carboxylateHMDB
D1-Pyrroline 2-carboxylic acidHMDB
delta-1-Pyrroline-2-carboxylateHMDB
1,2-DidehydroprolineHMDB
1-Pyrroline-2-carboxylic acidHMDB
delta1-Pyrroline-2-carboxylic acidHMDB
Δ1-Pyrroline-2-carboxylic acidHMDB
Chemical FormulaC5H7NO2
Average Molecular Weight113.1146
Monoisotopic Molecular Weight113.047678473
IUPAC Name3,4-dihydro-2H-pyrrol-1-ium-5-carboxylate
Traditional Name4,5-dihydro-3H-pyrrol-1-ium-2-carboxylate
CAS Registry Number2139-03-9
SMILES
OC(=O)C1=NCCC1
InChI Identifier
InChI=1S/C5H7NO2/c7-5(8)4-2-1-3-6-4/h1-3H2,(H,7,8)
InChI KeyRHTAIKJZSXNELN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolines. Pyrrolines are compounds containing a pyrroline ring, which is a five-member unsaturated aliphatic ring with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPyrrolines
Sub ClassNot Available
Direct ParentPyrrolines
Alternative Parents
Substituents
  • Pyrroline
  • Ketimine
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Imine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility9.26 g/LALOGPS
logP0.25ALOGPS
logP0.53ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)3.93ChemAxon
pKa (Strongest Basic)1.72ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.1 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity49.89 m³·mol⁻¹ChemAxon
Polarizability10.81 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+122.84231661259
DarkChem[M-H]-115.15531661259
DeepCCS[M+H]+128.37930932474
DeepCCS[M-H]-126.02130932474
DeepCCS[M-2H]-161.79930932474
DeepCCS[M+Na]+136.69330932474
AllCCS[M+H]+123.532859911
AllCCS[M+H-H2O]+118.632859911
AllCCS[M+NH4]+128.032859911
AllCCS[M+Na]+129.332859911
AllCCS[M-H]-120.232859911
AllCCS[M+Na-2H]-122.732859911
AllCCS[M+HCOO]-125.532859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.2.04 minutes32390414
Predicted by Siyang on May 30, 20229.3605 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.87 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid174.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid748.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid329.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid98.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid215.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid86.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid276.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid316.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)197.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid681.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid183.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid885.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid207.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid235.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate540.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA292.7 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water188.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
1-Pyrroline-2-carboxylic acidOC(=O)C1=NCCC11925.2Standard polar33892256
1-Pyrroline-2-carboxylic acidOC(=O)C1=NCCC11069.2Standard non polar33892256
1-Pyrroline-2-carboxylic acidOC(=O)C1=NCCC11126.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
1-Pyrroline-2-carboxylic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)C1=NCCC11285.0Semi standard non polar33892256
1-Pyrroline-2-carboxylic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1=NCCC11489.2Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB02838
Phenol Explorer Compound IDNot Available
FooDB IDFDB024129
KNApSAcK IDNot Available
Chemspider ID389057
KEGG Compound IDC03564
BioCyc IDDELTA1-PYRROLINE_2-CARBOXYLATE
BiGG ID42087
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440046
PDB ID2PC
ChEBI ID36761
Food Biomarker OntologyNot Available
VMH ID1P2CBXL
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. D-amino-acid oxidase
General function:
Involved in D-amino-acid oxidase activity
Specific function:
Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
Gene Name:
DAO
Uniprot ID:
P14920
Molecular weight:
39473.75
Reactions
D-Proline + Oxygen → 1-Pyrroline-2-carboxylic acid + Hydrogen peroxidedetails