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Protein

5-phosphohydroxy-L-lysine phospho-lyase

Gene

PHYKPL

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the pyridoxal-phosphate-dependent breakdown of 5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic phosphate and 2-aminoadipate semialdehyde.1 Publication

Catalytic activityi

(5R)-5-phosphonooxy-L-lysine + H2O = (S)-2-amino-6-oxohexanoate + NH3 + phosphate.

Cofactori

pyridoxal 5'-phosphate1 Publication

Kineticsi

  1. KM=16 µM for 5-phosphohydroxy-L-lysine (at 30 degrees Celsius)1 Publication
  1. Vmax=256 nmol/min/mg enzyme1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aminotransferase, Lyase, Transferase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

ReactomeiR-HSA-1442490. Collagen degradation.
R-HSA-71064. Lysine catabolism.

Names & Taxonomyi

Protein namesi
Recommended name:
5-phosphohydroxy-L-lysine phospho-lyase (EC:4.2.3.134)
Alternative name(s):
Alanine--glyoxylate aminotransferase 2-like 2
Gene namesi
Name:PHYKPL
Synonyms:AGXT2L2
ORF Names:PP9286
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:28249. PHYKPL.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Phosphohydroxylysinuria (PHLU)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA condition characterized by elevated phosphohydroxylysine in the urine. There is no clinical phenotype associated with this finding other than the urinary metabolites.
See also OMIM:615011
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti240 – 2401G → R in PHLU. 1 Publication
Corresponds to variant rs201105857 [ dbSNP | Ensembl ].
VAR_069543
Natural varianti437 – 4371E → V in PHLU. 2 Publications
Corresponds to variant rs142181517 [ dbSNP | Ensembl ].
VAR_069544

Keywords - Diseasei

Disease mutation

Organism-specific databases

MalaCardsiPHYKPL.
MIMi615011. phenotype.
PharmGKBiPA162376015.

Chemistry

DrugBankiDB00160. L-Alanine.

Polymorphism and mutation databases

DMDMi74750645.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 4504505-phosphohydroxy-L-lysine phospho-lyasePRO_0000287667Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei278 – 2781N6-(pyridoxal phosphate)lysineBy similarity

Proteomic databases

EPDiQ8IUZ5.
MaxQBiQ8IUZ5.
PaxDbiQ8IUZ5.
PRIDEiQ8IUZ5.

PTM databases

iPTMnetiQ8IUZ5.
PhosphoSiteiQ8IUZ5.

Expressioni

Gene expression databases

BgeeiQ8IUZ5.
CleanExiHS_AGXT2L2.
ExpressionAtlasiQ8IUZ5. baseline and differential.
GenevisibleiQ8IUZ5. HS.

Organism-specific databases

HPAiHPA036461.

Interactioni

Subunit structurei

Homotetramer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
POT1Q9NUX52EBI-751947,EBI-752420
USO1O607633EBI-751947,EBI-356164
VAC14Q08AM63EBI-751947,EBI-2107455

GO - Molecular functioni

Protein-protein interaction databases

BioGridi124425. 7 interactions.
IntActiQ8IUZ5. 5 interactions.
MINTiMINT-1441286.
STRINGi9606.ENSP00000310978.

Structurei

3D structure databases

ProteinModelPortaliQ8IUZ5.
SMRiQ8IUZ5. Positions 30-420.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1403. Eukaryota.
COG0160. LUCA.
GeneTreeiENSGT00530000062907.
HOGENOMiHOG000020206.
HOVERGENiHBG004196.
InParanoidiQ8IUZ5.
KOiK18202.
OMAiHPIACVA.
OrthoDBiEOG79KPF2.
PhylomeDBiQ8IUZ5.
TreeFamiTF320468.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 2 hits.
InterProiIPR005814. Aminotrans_3.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11986. PTHR11986. 1 hit.
PfamiPF00202. Aminotran_3. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8IUZ5-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAADQRPKAD TLALRQRLIS SSCRLFFPED PVKIVRAQGQ YMYDEQGAEY
60 70 80 90 100
IDCISNVAHV GHCHPLVVQA AHEQNQVLNT NSRYLHDNIV DYAQRLSETL
110 120 130 140 150
PEQLCVFYFL NSGSEANDLA LRLARHYTGH QDVVVLDHAY HGHLSSLIDI
160 170 180 190 200
SPYKFRNLDG QKEWVHVAPL PDTYRGPYRE DHPNPAMAYA NEVKRVVSSA
210 220 230 240 250
QEKGRKIAAF FAESLPSVGG QIIPPAGYFS QVAEHIRKAG GVFVADEIQV
260 270 280 290 300
GFGRVGKHFW AFQLQGKDFV PDIVTMGKSI GNGHPVACVA ATQPVARAFE
310 320 330 340 350
ATGVEYFNTF GGSPVSCAVG LAVLNVLEKE QLQDHATSVG SFLMQLLGQQ
360 370 380 390 400
KIKHPIVGDV RGVGLFIGVD LIKDEATRTP ATEEAAYLVS RLKENYVLLS
410 420 430 440 450
TDGPGRNILK FKPPMCFSLD NARQVVAKLD AILTDMEEKV RSCETLRLQP
Length:450
Mass (Da):49,711
Last modified:March 1, 2003 - v1
Checksum:i5EB28A6BDD44C429
GO
Isoform 2 (identifier: Q8IUZ5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-343: Missing.

Show »
Length:107
Mass (Da):11,924
Checksum:i7BA80D803EBD1F58
GO
Isoform 3 (identifier: Q8IUZ5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-275: Missing.

Show »
Length:175
Mass (Da):18,857
Checksum:i3E8449C54F503592
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti126 – 1261H → R.
Corresponds to variant rs7707147 [ dbSNP | Ensembl ].
VAR_048233
Natural varianti240 – 2401G → R in PHLU. 1 Publication
Corresponds to variant rs201105857 [ dbSNP | Ensembl ].
VAR_069543
Natural varianti437 – 4371E → V in PHLU. 2 Publications
Corresponds to variant rs142181517 [ dbSNP | Ensembl ].
VAR_069544

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 343343Missing in isoform 2. 1 PublicationVSP_025585Add
BLAST
Alternative sequencei1 – 275275Missing in isoform 3. 2 PublicationsVSP_025584Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF318375 mRNA. Translation: AAL55882.1.
AK023470 mRNA. Translation: BAG51198.1.
AK292061 mRNA. Translation: BAF84750.1.
AC136601 Genomic DNA. No translation available.
AC136632 Genomic DNA. No translation available.
CH471165 Genomic DNA. Translation: EAW53836.1.
CH471165 Genomic DNA. Translation: EAW53841.1.
BC008009 mRNA. Translation: AAH08009.1.
BC037567 mRNA. Translation: AAH37567.1.
BC110335 mRNA. Translation: AAI10336.1.
CCDSiCCDS4434.1. [Q8IUZ5-1]
RefSeqiNP_001265275.1. NM_001278346.1.
NP_699204.1. NM_153373.3. [Q8IUZ5-1]
UniGeneiHs.248746.

Genome annotation databases

EnsembliENST00000308158; ENSP00000310978; ENSG00000175309. [Q8IUZ5-1]
GeneIDi85007.
KEGGihsa:85007.
UCSCiuc003miz.5. human. [Q8IUZ5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF318375 mRNA. Translation: AAL55882.1.
AK023470 mRNA. Translation: BAG51198.1.
AK292061 mRNA. Translation: BAF84750.1.
AC136601 Genomic DNA. No translation available.
AC136632 Genomic DNA. No translation available.
CH471165 Genomic DNA. Translation: EAW53836.1.
CH471165 Genomic DNA. Translation: EAW53841.1.
BC008009 mRNA. Translation: AAH08009.1.
BC037567 mRNA. Translation: AAH37567.1.
BC110335 mRNA. Translation: AAI10336.1.
CCDSiCCDS4434.1. [Q8IUZ5-1]
RefSeqiNP_001265275.1. NM_001278346.1.
NP_699204.1. NM_153373.3. [Q8IUZ5-1]
UniGeneiHs.248746.

3D structure databases

ProteinModelPortaliQ8IUZ5.
SMRiQ8IUZ5. Positions 30-420.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124425. 7 interactions.
IntActiQ8IUZ5. 5 interactions.
MINTiMINT-1441286.
STRINGi9606.ENSP00000310978.

Chemistry

DrugBankiDB00160. L-Alanine.

PTM databases

iPTMnetiQ8IUZ5.
PhosphoSiteiQ8IUZ5.

Polymorphism and mutation databases

DMDMi74750645.

Proteomic databases

EPDiQ8IUZ5.
MaxQBiQ8IUZ5.
PaxDbiQ8IUZ5.
PRIDEiQ8IUZ5.

Protocols and materials databases

DNASUi85007.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000308158; ENSP00000310978; ENSG00000175309. [Q8IUZ5-1]
GeneIDi85007.
KEGGihsa:85007.
UCSCiuc003miz.5. human. [Q8IUZ5-1]

Organism-specific databases

CTDi85007.
GeneCardsiPHYKPL.
H-InvDBHIX0164247.
HGNCiHGNC:28249. PHYKPL.
HPAiHPA036461.
MalaCardsiPHYKPL.
MIMi614683. gene.
615011. phenotype.
neXtProtiNX_Q8IUZ5.
PharmGKBiPA162376015.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1403. Eukaryota.
COG0160. LUCA.
GeneTreeiENSGT00530000062907.
HOGENOMiHOG000020206.
HOVERGENiHBG004196.
InParanoidiQ8IUZ5.
KOiK18202.
OMAiHPIACVA.
OrthoDBiEOG79KPF2.
PhylomeDBiQ8IUZ5.
TreeFamiTF320468.

Enzyme and pathway databases

ReactomeiR-HSA-1442490. Collagen degradation.
R-HSA-71064. Lysine catabolism.

Miscellaneous databases

GenomeRNAii85007.
PROiQ8IUZ5.
SOURCEiSearch...

Gene expression databases

BgeeiQ8IUZ5.
CleanExiHS_AGXT2L2.
ExpressionAtlasiQ8IUZ5. baseline and differential.
GenevisibleiQ8IUZ5. HS.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 2 hits.
InterProiIPR005814. Aminotrans_3.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PANTHERiPTHR11986. PTHR11986. 1 hit.
PfamiPF00202. Aminotran_3. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
PROSITEiPS00600. AA_TRANSFER_CLASS_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Large-scale cDNA transfection screening for genes related to cancer development and progression."
    Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X.
    , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
    Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3), VARIANT VAL-437.
    Tissue: Placenta and Stomach.
  3. "The DNA sequence and comparative analysis of human chromosome 5."
    Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.
    , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
    Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
    Tissue: Brain, Muscle and Pancreas.
  6. "Molecular identification of hydroxylysine kinase and of ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and phosphoethanolamine."
    Veiga-da-Cunha M., Hadi F., Balligand T., Stroobant V., Van Schaftingen E.
    J. Biol. Chem. 287:7246-7255(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
  7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. Cited for: VARIANTS PHLU ARG-240 AND VAL-437.

Entry informationi

Entry nameiAT2L2_HUMAN
AccessioniPrimary (citable) accession number: Q8IUZ5
Secondary accession number(s): A8K7P6
, B3KN36, D3DWP9, Q8WYS6, Q96HW8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 15, 2007
Last sequence update: March 1, 2003
Last modified: June 8, 2016
This is version 125 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Caution

Does not seem to possess aminotransferase activity.1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.