We are currently updating the database - data may be missing for the next 10 minutes. We apologize for any inconvenience.

Human Metabolome Database Version 2.5

 

Showing metabocard for 4-Hydroxy-L-proline (HMDB06055)

Legend: metabolite field enzyme field

Version 2.5
Creation Date 2007-04-12 22:28:41
Update Date 2009-12-14 14:59:06
Accession Number HMDB06055
Secondary Accession Numbers Not Available
Common Name 4-Hydroxy-L-proline
Description A hydroxylated form of the imino acid proline. A deficiency in ascorbic acid can result in impaired hydroxyproline formation. (PubChem CID:69248)
Synonyms
  1. L-4-hydroxy-proline
  2. L-4-Hydroxyproline
  3. L-4-allo-hydroxy-Proline
  4. 4-hydroxy-L-Proline
  5. cis-4-hydroxy-L-Proline
  6. cis-4-hydroxyproline;(2S)-4-hydroxypyrrolidine-2-carboxylic acid
  7. (4S)-4-hydroxy-L-Proline
  8. allo-4-Hydroxy-L-proline
  9. allo-4-Hydroxyproline
  10. allo-hydroxy-L-Proline
  11. L-Allohydroxyproline
Chemical IUPAC Name (2S)-4-hydroxypyrrolidine-2-carboxylic acid
Chemical Formula C5H9NO3
Chemical Structure Structure
Chemical Taxonomy
Kingdom
  • Organic
Super Class
  • Amino acids and Amino Acid conjugates
Class
  • Amino Acids
Sub Class
  • NA
Family
  • Mammalian Metabolite
Species
  • secondary alcohol
  • 1,2-aminoalcohol
  • secondary amine
  • secondary aliphatic amine (dialkylamine)
  • carboxylic acid
  • heterocyclic compound
  • alpha-aminoacid
Biofunction
—
Application
—
Source
  • Endogenous
Average Molecular Weight 131.130
Monoisotopic Molecular Weight 131.058243
Isomeric SMILES OC1CN[C@@H](C1)C(O)=O
Canonical SMILES OC1CNC(C1)C(O)=O
KEGG Compound ID C01015 Link Image
BioCyc ID Protein-hydroxyprolines Link Image
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB06055 Link Image
Metagene Link HMDB06055 Link Image
METLIN ID Not Available
PubChem Compound 69248 Link Image
PubChem Substance 10366583 Link Image
ChEBI ID 18240 Link Image
CAS Registry Number 30724-02-8
InChI Identifier InChI=1/C5H9NO3/c7-3-1-4(5(8)9)6-2-3/h3-4,6-7H,1-2H2,(H,8,9)/t3?,4-/m0/s1
Synthesis Reference Not Available
Melting Point (Experimental) 274 oC
Experimental Water Solubility 361 mg/mL at 25 oC [MERCK INDEX (1996)] Source: PhysProp
Predicted Water Solubility 492.0 mg/mL [Predicted by ALOGPS] Calculated using ALOGPS
Physiological Charge 0
State Solid
Experimental LogP/Hydrophobicity -3.17 [HANSCH,C ET AL. (1995)] Source: PhysProp
Predicted LogP/Hydrophobicity -3.31 [Predicted by ALOGPS]; -3.4 [Predicted by PubChem via XLOGP] Calculated using ALOGPS
Material Safety Data Sheet (MSDS)
MOL File Show
SDF File Show
PDB File Show
2D Structure
3D Structure
Experimental PDB ID Not Available
Experimental 1H NMR Spectrum Not Available
Experimental 13C NMR Spectrum Not Available
Experimental 13C HSQC Spectrum Not Available
Predicted 1H NMR Spectrum Not Available
Not Available
Predicted 13C NMR Spectrum Not Available
Not Available
Mass Spectrum Not Available
Simplified TOCSY Spectrum Not Available
BMRB Spectrum Not Available
Cellular Location Not Available
Biofluid Location
  • Blood
  • Cerebrospinal Fluid
  • Urine
Tissue Location Not Available
Concentrations (Normal)
Biofluid Urine
Value 0.15 umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Patient information Normal
Comments Not Available
References
  • Guo K, Li L: Differential (12)C-/(13)C-Isotope Dansylation Labeling and Fast Liquid Chromatography/Mass Spectrometry for Absolute and Relative Quantification of the Metabolome. Anal Chem. 2009 Mar 23. [PubMed Link Image]
Concentrations (Abnormal)
Biofluid Blood
Value 5.6 +/- 0.67 uM
Age Adult:>18 yrs old
Sex Both
Condition Alzheimer's disease
Comments Not Available
References
  • Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed Link Image]
Biofluid CSF
Value 0.28 +/- 0.055 uM
Age Adult:>18 yrs old
Sex Both
Condition Alzheimer's disease
Comments Not Available
References
  • Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed Link Image]
Biofluid Urine
Value 0.21 +/- 0.017 umol/mmol creatinine
Age Adult:>18 yrs old
Sex Both
Condition Alzheimer's disease
Comments Not Available
References
  • Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed Link Image]
Associated Disorders
Condition References
Alzheimer's disease
  • Fonteh AN, Harrington RJ, Tsai A, Liao P, Harrington MG: Free amino acid and dipeptide changes in the body fluids from Alzheimer's disease subjects. Amino Acids. 2007 Feb;32(2):213-24. Epub 2006 Oct 10. [PubMed Link Image]
OMIM ID
Pathways
Name SMPDB Link KEGG Link
Arginine and Proline Metabolism SMP00020 Link Image map00330 Link Image
General References
  1. Tasanen K, Eble JA, Aumailley M, Schumann H, Baetge J, Tu H, Bruckner P, Bruckner-Tuderman L: Collagen XVII is destabilized by a glycine substitution mutation in the cell adhesion domain Col15. J Biol Chem. 2000 Feb 4;275(5):3093-9. [PubMed Link Image]
  2. Keskiaho K, Hieta R, Sormunen R, Myllyharju J: Chlamydomonas reinhardtii has multiple prolyl 4-hydroxylases, one of which is essential for proper cell wall assembly. Plant Cell. 2007 Jan;19(1):256-69. Epub 2007 Jan 12. [PubMed Link Image]
  3. Lafranconi WM, Duhamel RC, Brendel K, Huxtable RJ: Differentiation of the cardiac and pulmonary toxicity of monocrotaline, a pyrrolizidine alkaloid. Biochem Pharmacol. 1984 Jan 15;33(2):191-7. [PubMed Link Image]
  4. Sodian R, Hoerstrup SP, Sperling JS, Martin DP, Daebritz S, Mayer JE Jr, Vacanti JP: Evaluation of biodegradable, three-dimensional matrices for tissue engineering of heart valves. ASAIO J. 2000 Jan-Feb;46(1):107-10. [PubMed Link Image]
  5. ADAMS E, GOLDSTONE A, SINGH RM, ROSSO G: SUBSTRATE ACTIVITY OF 3-HYDROXYPROLINE ISOMERS FOR ENZYMES ACTIVE WITH 4-HYDROXYPROLINE. Biochim Biophys Acta. 1964 Jul 8;89:164-6. [PubMed Link Image]
  6. Last JA, Reiser KM, Tyler WS, Rucker RB: Long-term consequences of exposure to ozone. I. Lung collagen content. Toxicol Appl Pharmacol. 1984 Jan;72(1):111-8. [PubMed Link Image]
  7. Koike K, Li Y, Seo M, Sakurada I, Tezuka K, Uchikura K: Free 4-hydroxyproline content in serum of bedridden aged people is elevated due to fracture. Biol Pharm Bull. 2000 Jan;23(1):101-3. [PubMed Link Image]
  8. Burjanadze TV: New analysis of the phylogenetic change of collagen thermostability. Biopolymers. 2000 May;53(6):523-8. [PubMed Link Image]
  9. Dixon IM, Hao J, Reid NL, Roth JC: Effect of chronic AT(1) receptor blockade on cardiac Smad overexpression in hereditary cardiomyopathic hamsters. Cardiovasc Res. 2000 May;46(2):286-97. [PubMed Link Image]
  10. Turpeenniemi-Hujanen T, Myllyla R: Concomitant hydroxylation of proline and lysine residues in collagen using purified enzymes in vitro. Biochim Biophys Acta. 1984 Jul 16;800(1):59-65. [PubMed Link Image]
Metabolic Enzymes
  1. D-amino-acid oxidase
  2. cDNA FLJ75752, highly similar to Homo sapiens pyrroline-5-carboxylate reductase family, member 2
  3. Uncharacterized protein PRODH
  4. Melastatin 1 splicing variant
Enzyme 1 [top]
Enzyme 1 ID 5438
Enzyme 1 Name D-amino-acid oxidase
Enzyme 1 Synonyms
  1. DAMOX
  2. DAO
  3. DAAO
Enzyme 1 Gene Name DAO
Enzyme 1 Protein Sequence >D-amino-acid oxidase 
MRVVVIGAGVIGLSTALCIHERYHSVLQPLDIKVYADRFTPLTTTDVAAGLWQPYLSDPN
NPQEADWSQQTFDYLLSHVHSPNAENLGLFLISGYNLFHEAIPDPSWKDTVLGFRKLTPR
ELDMFPDYGYGWFHTSLILEGKNYLQWLTERLTERGVKFFQRKVESFEEVAREGADVIVN
CTGVWAGALQRDPLLQPGRGQIMKVDAPWMKHFILTHDPERGIYNSPYIIPGTQTVTLGG
IFQLGNWSELNNIQDHNTIWEGCCRLEPTLKNARIIGERTGFRPVRPQIRLEREQLRTGP
SNTEVIHNYGHGGYGLTIHWGCALEAAKLFGRILEEKKLSRMPPSHL
Enzyme 1 Number of Residues 347
Enzyme 1 Molecular Weight 39475
Enzyme 1 Theoretical pI 6.84
Enzyme 1 GO Classification
Function
  • D-amino-acid oxidase activity
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH2 group of donors
  • oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
Process
  • cellular metabolism
  • electron transport
  • generation of precursor metabolites and energy
  • metabolism
  • physiological process
Component
—
Enzyme 1 General Function Amino acid transport and metabolism
Enzyme 1 Specific Function 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
Enzyme 1 Pathways
  • Arginine and Proline Metabolism (map00330 Link Image)
  • D-Arginine and D-ornithine Metabolism (map00472 Link Image)
  • Glycine, Serine and Threonine Metabolism (map00260 Link Image)
Enzyme 1 Reactions
  • a D-amino acid + H2O + O2 = a 2-oxo acid + ammonia + H2O2
Enzyme 1 Pfam Domain Function
Enzyme 1 Signals
  • 1-16
Enzyme 1 Transmembrane Regions Not Available
Enzyme 1 Essentiality Not Available
Enzyme 1 GenBank ID Protein 30446 Link Image
Enzyme 1 UniProtKB/Swiss-Prot ID P14920 Link Image
Enzyme 1 UniProtKB/Swiss-Prot Entry Name OXDA_HUMAN Link Image
Enzyme 1 PDB ID Not Available
Enzyme 1 Cellular Location Not Available
Enzyme 1 Gene Sequence >1044 bp 
ATGCGTGTGGTGGTGATTGGAGCAGGAGTCATCGGGCTGTCCACCGCCCTCTGCATCCAT
GAGCGCTACCACTCAGTCCTGCAGCCACTGCACATAAAGGTCTACGCGGACCGCTTCACC
CCACTCACCACCACCGACGTGGCTGCCGGCCTCTGGCAGCCCTACCTTTCTGACCCCAAC
AACCCACAGGAGGCGGACTGGAGCCAACAGACCTTTGACTATCTCCTGAGCCATGTCCAT
TCTCCCAACGCTGAAAACCTGGGCCTGTTCCTAATCTCGGGCTACAACCTCTTCCATGAA
GCCATTCCGGACCCTTCCTGGAAGGACACAGTTCTGGGATTTCGGAAGCTGACCCCCAGA
GAGCTGGATATGTTCCCAGATTACGGCTATGGCTGGTTCCACACAAGCCTAATTCTGGAG
GGAAAGAACTATCTACAGTGGCTGACTGAAAGGTTAACTGAGAGGGGAGTGAAGTTCTTC
CAGCGGAAAGTGGAGTCTTTTGAGGAGGTGGCAAGAGAAGGCGCAGACGTGATTGTCAAC
TGCACTGGGGTATGGGCTGGGGCGCTACAACGAGACCCCCTGCTGCAGCCAGGCCGGGGG
CAGATCATGAAGGTGGACGCCCCTTGGATGAAGCACTTCATTCTCACCCATGACCCAGAG
AGAGGCATCTACAATTCCCCGTACATCATCCCAGGGACCCAGACAGTTACTCTTGGAGGC
ATCTTCCAGTTGGGAAACTGGAGTGAACTAAACAATATCCAGGACCACAACACCATTTGG
GAAGGCTGCTGCAGACTGGAGCCCACACTGAAGAATGCAAGAATTATTGGTGAAGCAACT
GGCTTCCGGCCAGTACGCCCCCAGATTCGGCTAGAAAGAGAACAGCTTCGCACTGGACCT
TCAAACACAGAGGTCATCCACAACTATGGCCATGGAGGCTACGGGCTCACCATCCACTGG
GGATGTGCCCTGGAGGCAGCCAAGCTCTTTGGGAGAATCCTGGAAGAAAAGAAATTGTCC
AGAATGCCACCATCCCACCTCTGA
Enzyme 1 GenBank Gene ID X13227 Link Image
Enzyme 1 GeneCard ID DAO Link Image
Enzyme 1 GenAtlas ID DAO Link Image
Enzyme 1 HGNC ID HGNC:2671 Link Image
Enzyme 1 Chromosome Location 12
Enzyme 1 Locus 12q24
Enzyme 1 SNPs SNPJam Report Link Image
Enzyme 1 General References
  1. Momoi K, Fukui K, Watanabe F, Miyake Y: Molecular cloning and sequence analysis of cDNA encoding human kidney D-amino acid oxidase. FEBS Lett. 1988 Sep 26;238(1):180-4. [PubMed Link Image]
  2. Fukui K, Miyake Y: Molecular cloning and chromosomal localization of a human gene encoding D-amino-acid oxidase. J Biol Chem. 1992 Sep 15;267(26):18631-8. [PubMed Link Image]
Enzyme 1 Metabolite References Not Available
Enzyme 2 [top]
Enzyme 2 ID 12995
Enzyme 2 Name cDNA FLJ75752, highly similar to Homo sapiens pyrroline-5-carboxylate reductase family, member 2
Enzyme 2 Synonyms
  1. PYCR2, mRNA
  2. Pyrroline-5-carboxylate reductase family, member 2, isoform CRA_b
Enzyme 2 Gene Name PYCR2
Enzyme 2 Protein Sequence >cDNA FLJ75752, highly similar to Homo sapiens pyrroline-5-carboxylate reductase family, member 2 
MSVGFIGAGQLAYALARGFTAAGILSAHKIIASSPEMNLPTVSALRKMGVNLTRSNKETV
KHSDVLFLAVKPHIIPFILDEIGADVQARHIVVSCAAGVTISSVEKKLMAFQPAPKVIRC
MTNTPVVVQEGATVYATGTHALVEDGQLLEQLMSSVGFCTEVEEDLIDAVTGLSGSGPAY
AFMALDALADGGVKMGLPRRLAIQLGAQALLGAAKMLLDSEQHPCQLKDNVCSPGGATIH
ALHFLESGGFRSLLINAVEASCIRTRELQSMADQEKISPAALKKTLLDRVKLESPTVSTL
TPSSPGKLLTRSLALGGKKD
Enzyme 2 Number of Residues 320
Enzyme 2 Molecular Weight 33638
Enzyme 2 Theoretical pI 7.87
Enzyme 2 GO Classification Not Available
Enzyme 2 General Function Amino acid transport and metabolism
Enzyme 2 Specific Function Not Available
Enzyme 2 Pathways Not Available
Enzyme 2 Reactions Not Available
Enzyme 2 Pfam Domain Function Not Available
Enzyme 2 Signals
  • None
Enzyme 2 Transmembrane Regions
  • None
Enzyme 2 Essentiality Not Available
Enzyme 2 GenBank ID Protein 158257258 Link Image
Enzyme 2 UniProtKB/Swiss-Prot ID A8K798 Link Image
Enzyme 2 UniProtKB/Swiss-Prot Entry Name A8K798_HUMAN Link Image
Enzyme 2 PDB ID Not Available
Enzyme 2 Cellular Location Not Available
Enzyme 2 Gene Sequence Not Available
Enzyme 2 GenBank Gene ID AK291913 Link Image
Enzyme 2 GeneCard ID A8K798 Link Image
Enzyme 2 GenAtlas ID Not Available
Enzyme 2 HGNC ID Not Available
Enzyme 2 Chromosome Location Not Available
Enzyme 2 Locus Not Available
Enzyme 2 SNPs SNPJam Report Link Image
Enzyme 2 General References Not Available
Enzyme 2 Metabolite References Not Available
Enzyme 3 [top]
Enzyme 3 ID 12996
Enzyme 3 Name Uncharacterized protein PRODH
Enzyme 3 Synonyms Not Available
Enzyme 3 Gene Name PRODH
Enzyme 3 Protein Sequence >Uncharacterized protein PRODH 
RHGSEARPARAAPLHSPLRPAVHGAGLPRAARSGPSGRARRWVGHGSAAAGARRGLRQRA
GGVPQPANLGAGAEPAGAALVRLARAAGAPRAAAVCFQETSRTEAIQQAHEDDLLWAFCS
RGGESIQPLLRHYRAFGVSAILDYGVEEDLSPEEAEHKEMESCTSAAERDGSGTNKRDKQ
YQAHWAFGDRRNGVISARTYFYANEAKCDSHMETFLRCIEASGRVSDDGFIAIKLTALGR
PQFLLQFSEVLAKWRCFFHQMAVEQGQAGLAAMDTKLEVAVLQESVAKLGIASRAEIEDW
FTAETLGVSGTMDLLDWSSLIDSRTKLSKHLVVPNAQTGQLEPLLSRFTEEEELQMTRML
QRMDVLAKKATEMGVRLMVDAEQTYFQPAISRLTLEMQRKFNVEKPLIFNTYQPHPADAY
DNVTLDVELARREGWCFGAKLVRGAYLAQERARAAEIGYEDPINPTYEATNAMYHRCLDY
VLEELKHNAKAKVMVASHNEDTVRFALRRMEELGLHPADHRVYFGQLLGMCDQISFPLGQ
AGYPVYKYVPYGPVMEVLPYLSRRALENSSLMKGTHRERQLLWLELLRRLRTGNLFHRPA
Enzyme 3 Number of Residues 600
Enzyme 3 Molecular Weight 66921
Enzyme 3 Theoretical pI 8.01
Enzyme 3 GO Classification
Function
  • catalytic activity
  • oxidoreductase activity
  • oxidoreductase activity, acting on the CH-NH group of donors
  • proline dehydrogenase activity
Process
  • amino acid and derivative metabolism
  • amino acid metabolism
  • cellular metabolism
  • glutamate biosynthesis
  • glutamate metabolism
  • glutamine family amino acid metabolism
  • metabolism
  • physiological process
  • proline catabolism
  • proline metabolism
Component
—
Enzyme 3 General Function Amino acid transport and metabolism
Enzyme 3 Specific Function Not Available
Enzyme 3 Pathways Not Available
Enzyme 3 Reactions Not Available
Enzyme 3 Pfam Domain Function
Enzyme 3 Signals
  • None
Enzyme 3 Transmembrane Regions
  • None
Enzyme 3 Essentiality Not Available
Enzyme 3 GenBank ID Protein Not Available
Enzyme 3 UniProtKB/Swiss-Prot ID A6NF53 Link Image
Enzyme 3 UniProtKB/Swiss-Prot Entry Name A6NF53_HUMAN Link Image
Enzyme 3 PDB ID Not Available
Enzyme 3 Cellular Location Not Available
Enzyme 3 Gene Sequence Not Available
Enzyme 3 GenBank Gene ID AC007326 Link Image
Enzyme 3 GeneCard ID A6NF53 Link Image
Enzyme 3 GenAtlas ID PRODH Link Image
Enzyme 3 HGNC ID HGNC:9453 Link Image
Enzyme 3 Chromosome Location Not Available
Enzyme 3 Locus Not Available
Enzyme 3 SNPs SNPJam Report Link Image
Enzyme 3 General References
  1. Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, O'Brien KP, et al.: The DNA sequence of human chromosome 22. Nature. 1999 Dec 2;402(6761):489-95. [PubMed Link Image]
Enzyme 3 Metabolite References Not Available
Enzyme 4 [top]
Enzyme 4 ID 12997
Enzyme 4 Name Melastatin 1 splicing variant
Enzyme 4 Synonyms Not Available
Enzyme 4 Gene Name MLSN1
Enzyme 4 Protein Sequence >Melastatin 1 splicing variant 
MYIRVSYDTKPDSLLHLMVKDWQLELPKLLISVHGGLQNFEMQPKLKQVFGKGLIKAAMT
TGAWIFTGGVSTGVISHVGDALKDHSSKSRGRVCAIGIAPWGIVENKEDLVGKDVTRVYQ
TMSNPLSKLSVLNNSHTHFILADNGTLGKYGAEVKLRRLLEKHISLQKINTRLGQGVPLV
GLVVEGGPNVVSIVLEYLQEEPPIPVVICDGSGRASDILSFAHKYCEEGG
Enzyme 4 Number of Residues 230
Enzyme 4 Molecular Weight 25053
Enzyme 4 Theoretical pI 8.79
Enzyme 4 GO Classification Not Available
Enzyme 4 General Function Not Available
Enzyme 4 Specific Function Not Available
Enzyme 4 Pathways Not Available
Enzyme 4 Reactions Not Available
Enzyme 4 Pfam Domain Function Not Available
Enzyme 4 Signals
  • None
Enzyme 4 Transmembrane Regions
  • None
Enzyme 4 Essentiality Not Available
Enzyme 4 GenBank ID Protein 33235690 Link Image
Enzyme 4 UniProtKB/Swiss-Prot ID Q7Z4N3 Link Image
Enzyme 4 UniProtKB/Swiss-Prot Entry Name Q7Z4N3_HUMAN Link Image
Enzyme 4 PDB ID Not Available
Enzyme 4 Cellular Location Not Available
Enzyme 4 Gene Sequence Not Available
Enzyme 4 GenBank Gene ID AB115500 Link Image
Enzyme 4 GeneCard ID Q7Z4N3 Link Image
Enzyme 4 GenAtlas ID TRPM1 Link Image
Enzyme 4 HGNC ID HGNC:7146 Link Image
Enzyme 4 Chromosome Location Not Available
Enzyme 4 Locus Not Available
Enzyme 4 SNPs SNPJam Report Link Image
Enzyme 4 General References Not Available
Enzyme 4 Metabolite References Not Available