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Showing metabocard for Ureidoisobutyric acid (HMDB0002031)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:33 UTC
Update Date2023-02-21 17:16:04 UTC
HMDB IDHMDB0002031
Secondary Accession Numbers
  • HMDB02031
Metabolite Identification
Common NameUreidoisobutyric acid
DescriptionUreidoisobutyric acid, also known as 3-ureidoisobutyrate or beta-UBA, belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group. Ureidoisobutyric acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Ureidoisobutyric acid exists in all living organisms, ranging from bacteria to humans. Within humans, ureidoisobutyric acid participates in a number of enzymatic reactions. In particular, ureidoisobutyric acid can be biosynthesized from dihydrothymine through its interaction with the enzyme dihydropyrimidinase. Outside of the human body, ureidoisobutyric acid has been detected, but not quantified in, several different foods, such as bread, squashberries, black elderberries, black crowberries, and climbing beans. This could make ureidoisobutyric acid a potential biomarker for the consumption of these foods. Ureidoisobutyric acid is increased in the urine of patients with beta-ureidopropionase (EC 3.5.1.6) deficiency (PMID: 12271438 ), a genetic disorder. Ureidoisobutyric acid can be used to predict a patient's individual phenotypes of enzyme deficiencies in pyrimidine metabolism when associated with a risk for severe toxicity against the antineoplastic agent 5-fluorouracil (PMID: 12798197 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002031 (Ureidoisobutyric acid)

  Mrv1652309042000262D          

 10  9  0  0  0  0            999 V2000
   15.3740   -4.1659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2316   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6605   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.1659    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.5173   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.9908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  2  0  0  0  0
  4  7  1  0  0  0  0
  4  9  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  6  0  0  0
  6 10  1  0  0  0  0
M  END
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3D MOL for HMDB0002031 (Ureidoisobutyric acid)

HMDB0002031
     RDKit          3D
Ureidoisobutyric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.1112    1.5219    0.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8818    0.7891   -0.2656 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1916    0.8164    0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451    0.2111    0.4747 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7366   -1.1415    0.2434 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0863   -1.5184   -0.0562 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8637   -2.0122    0.2909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.5511   -0.5682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0674   -1.1532    0.2810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0587   -1.1791   -1.7718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9759    1.2560   -0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2344    1.0776    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9498    2.5992    0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6128    1.3803   -1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3320    1.8888    1.1354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1640    0.3114    1.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3011    0.8749    0.4182 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8250   -0.8193   -0.1677 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3477   -2.5189   -0.1678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7117   -1.8327   -2.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  3 16  1  0
  4 17  1  0
  6 18  1  0
  6 19  1  0
 10 20  1  0
M  END
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3D SDF for HMDB0002031 (Ureidoisobutyric acid)

  Mrv1652309042000262D          

 10  9  0  0  0  0            999 V2000
   15.3740   -4.1659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -2.9284    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2316   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6605   -4.1659    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.1659    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   17.5173   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8028   -4.9908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9461   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0884   -3.7533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 10  1  0  0  0  0
  2  9  2  0  0  0  0
  3 10  2  0  0  0  0
  4  7  1  0  0  0  0
  4  9  1  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  6  0  0  0
  6 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002031

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H](CNC(N)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)/t3-/m0/s1

> <INCHI_KEY>
PHENTZNALBMCQD-VKHMYHEASA-N

> <FORMULA>
C5H10N2O3

> <MOLECULAR_WEIGHT>
146.1445

> <EXACT_MASS>
146.069142196

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.818860727118281

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-3-(carbamoylamino)-2-methylpropanoic acid

> <ALOGPS_LOGP>
-0.86

> <JCHEM_LOGP>
-0.882175473

> <ALOGPS_LOGS>
-0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.22016214605836

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.3229374248469945

> <JCHEM_PKA_STRONGEST_BASIC>
-1.7588206273546918

> <JCHEM_POLAR_SURFACE_AREA>
92.41999999999999

> <JCHEM_REFRACTIVITY>
33.3978

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-3-(carbamoylamino)-2-methylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0002031 (Ureidoisobutyric acid)

HMDB0002031
     RDKit          3D
Ureidoisobutyric acid
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.1112    1.5219    0.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8818    0.7891   -0.2656 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1916    0.8164    0.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451    0.2111    0.4747 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7366   -1.1415    0.2434 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0863   -1.5184   -0.0562 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8637   -2.0122    0.2909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3613   -0.5511   -0.5682 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0674   -1.1532    0.2810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0587   -1.1791   -1.7718 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9759    1.2560   -0.2868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2344    1.0776    1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9498    2.5992    0.3681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6128    1.3803   -1.1738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3320    1.8888    1.1354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1640    0.3114    1.7305 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3011    0.8749    0.4182 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8250   -0.8193   -0.1677 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3477   -2.5189   -0.1678 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7117   -1.8327   -2.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  6
  3 15  1  0
  3 16  1  0
  4 17  1  0
  6 18  1  0
  6 19  1  0
 10 20  1  0
M  END
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PDB for HMDB0002031 (Ureidoisobutyric acid)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0      28.698  -7.776   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      35.366  -5.466   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      30.032  -5.466   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      34.032  -7.776   0.000  0.00  0.00           N+0
HETATM    5  N   UNK     0      36.700  -7.776   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      31.365  -7.776   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      32.699  -7.006   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      31.365  -9.316   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      35.366  -7.006   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      30.032  -7.006   0.000  0.00  0.00           C+0
CONECT    1   10                                                            
CONECT    2    9                                                            
CONECT    3   10                                                            
CONECT    4    7    9                                                       
CONECT    5    9                                                            
CONECT    6    7    8   10                                                  
CONECT    7    4    6                                                       
CONECT    8    6                                                            
CONECT    9    2    4    5                                                  
CONECT   10    1    3    6                                                  
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0002031 (Ureidoisobutyric acid)

COMPND    HMDB0002031
HETATM    1  C1  UNL     1      -2.111   1.522   0.344  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.882   0.789  -0.266  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.192   0.816   0.769  1.00  0.00           C  
HETATM    4  N1  UNL     1       1.445   0.211   0.475  1.00  0.00           N  
HETATM    5  C4  UNL     1       1.737  -1.142   0.243  1.00  0.00           C  
HETATM    6  N2  UNL     1       3.086  -1.518  -0.056  1.00  0.00           N  
HETATM    7  O1  UNL     1       0.864  -2.012   0.291  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.361  -0.551  -0.568  1.00  0.00           C  
HETATM    9  O2  UNL     1      -2.067  -1.153   0.281  1.00  0.00           O  
HETATM   10  O3  UNL     1      -1.059  -1.179  -1.772  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.976   1.256  -0.287  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.234   1.078   1.350  1.00  0.00           H  
HETATM   13  H3  UNL     1      -1.950   2.599   0.368  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.613   1.380  -1.174  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.332   1.889   1.135  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.164   0.311   1.730  1.00  0.00           H  
HETATM   17  H7  UNL     1       2.301   0.875   0.418  1.00  0.00           H  
HETATM   18  H8  UNL     1       3.825  -0.819  -0.168  1.00  0.00           H  
HETATM   19  H9  UNL     1       3.348  -2.519  -0.168  1.00  0.00           H  
HETATM   20  H10 UNL     1      -1.712  -1.833  -2.175  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    8   14
CONECT    3    4   15   16
CONECT    4    5   17
CONECT    5    6    7    7
CONECT    6   18   19
CONECT    8    9    9   10
CONECT   10   20
END
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SMILES for HMDB0002031 (Ureidoisobutyric acid)

C[C@@H](CNC(N)=O)C(O)=O
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INCHI for HMDB0002031 (Ureidoisobutyric acid)

InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)/t3-/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
UreidoisobutyrateGenerator
(2S)-3-[(C-Hydroxycarbonimidoyl)amino]-2-methylpropanoateHMDB
(2S)-3-(Carbamoylamino)-2-methylpropanoic acidHMDB
(2S)-3-(Carbamoylamino)-2-methylpropionic acidHMDB
3-((Aminocarbonyl)amino)-2-methylpropanoic acidHMDB
3-((Aminocarbonyl)amino)-2-methylpropionic acidHMDB
3-UreidoisobutyrateHMDB
3-[(Aminocarbonyl)amino]-2-methylpropanoic acidHMDB
3-[(Aminocarbonyl)amino]-2-methylpropionic acidHMDB
beta-UBAHMDB
beta-Ureidoisobutyric acidHMDB
Β-ubaHMDB
Β-ureidoisobutyric acidHMDB
Chemical FormulaC5H10N2O3
Average Molecular Weight146.1445
Monoisotopic Molecular Weight146.069142196
IUPAC Name(2S)-3-(carbamoylamino)-2-methylpropanoic acid
Traditional Name(2S)-3-(carbamoylamino)-2-methylpropanoic acid
CAS Registry Number19140-82-0
SMILES
C[C@@H](CNC(N)=O)C(O)=O
InChI Identifier
InChI=1S/C5H10N2O3/c1-3(4(8)9)2-7-5(6)10/h3H,2H2,1H3,(H,8,9)(H3,6,7,10)/t3-/m0/s1
InChI KeyPHENTZNALBMCQD-VKHMYHEASA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ureas. Ureas are compounds containing two amine groups joined by a carbonyl (C=O) functional group.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic carbonic acids and derivatives
Sub ClassUreas
Direct ParentUreas
Alternative Parents
Substituents
  • Urea
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm (predicted from logP)
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
Cerebrospinal Fluid (CSF)Detected and Quantified0.01 +/- 0.05 uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified<0.9 umol/mmol creatinineInfant (0-1 year old)Both
Normal		 details
UrineDetected and Quantified0.113 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified1.4 - 5.9 uMAdult (>18 years old)BothBeta-ureidopropionase deficiency details
Associated Disorders and Diseases
Disease References
Beta-ureidopropionase deficiency
  1. van Kuilenburg AB, Meinsma R, Beke E, Assmann B, Ribes A, Lorente I, Busch R, Mayatepek E, Abeling NG, van Cruchten A, Stroomer AE, van Lenthe H, Zoetekouw L, Kulik W, Hoffmann GF, Voit T, Wevers RA, Rutsch F, van Gennip AH: beta-Ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities. Hum Mol Genet. 2004 Nov 15;13(22):2793-801. Epub 2004 Sep 22. [PubMed:15385443 ]
Associated OMIM IDs
  • 613161 (Beta-ureidopropionase deficiency)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022808
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC05100
BioCyc ID3-UREIDO-ISOBUTYRATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound88558720
PDB IDURQ
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH ID3UIB
MarkerDB IDMDB00000369
Good Scents IDNot Available
References
Synthesis ReferenceEvans, W. R.; Tsai, Chi Shiun; Axelrod, Bernard. Origin of b-aminoisobutyric acid in iris. Nature (London, United Kingdom) (1961), 190 809.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hofmann U, Schwab M, Seefried S, Marx C, Zanger UM, Eichelbaum M, Murdter TE: Sensitive method for the quantification of urinary pyrimidine metabolites in healthy adults by gas chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 5;791(1-2):371-80. [PubMed:12798197 ]
  2. Ohse M, Matsuo M, Ishida A, Kuhara T: Screening and diagnosis of beta-ureidopropionase deficiency by gas chromatographic/mass spectrometric analysis of urine. J Mass Spectrom. 2002 Sep;37(9):954-62. [PubMed:12271438 ]

Enzymes

Enzyme Details
1. Dihydropyrimidinase
General function:
Involved in hydrolase activity
Specific function:
Catalyzes the second step of the reductive pyrimidine degradation, the reversible hydrolytic ring opening of dihydropyrimidines. Can catalyze the ring opening of 5,6-dihydrouracil to N-carbamyl-alanine and of 5,6-dihydrothymine to N-carbamyl-amino isobutyrate.
Gene Name:
DPYS
Uniprot ID:
Q14117
Molecular weight:
56629.36
Reactions
Dihydrothymine + Water → Ureidoisobutyric aciddetails
Enzyme Details
2. Beta-ureidopropionase
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Specific function:
Converts N-carbamyl-beta-aminoisobutyric acid and N-carbamyl-beta-alanine to, respectively, beta-aminoisobutyric acid and beta-alanine, ammonia and carbon dioxide.
Gene Name:
UPB1
Uniprot ID:
Q9UBR1
Molecular weight:
43165.705
Reactions
Ureidoisobutyric acid + Water → 3-Aminoisobutanoic acid + Carbon dioxide + Ammoniadetails