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5-phosphohydroxy-L-lysine phospho-lyase (EC 4.2.3.134) (Alanine--glyoxylate aminotransferase 2-like 2)

 AT2L2_HUMAN             Reviewed;         450 AA.
Q8IUZ5; A8K7P6; B3KN36; D3DWP9; Q8WYS6; Q96HW8;
15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
12-SEP-2018, entry version 144.
RecName: Full=5-phosphohydroxy-L-lysine phospho-lyase;
EC=4.2.3.134;
AltName: Full=Alanine--glyoxylate aminotransferase 2-like 2;
Name=PHYKPL; Synonyms=AGXT2L2; ORFNames=PP9286;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
PubMed=15498874; DOI=10.1073/pnas.0404089101;
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.;
"Large-scale cDNA transfection screening for genes related to cancer
development and progression.";
Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3), AND VARIANT
VAL-437.
TISSUE=Placenta, and Stomach;
PubMed=14702039; DOI=10.1038/ng1285;
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.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=15372022; DOI=10.1038/nature02919;
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.;
"The DNA sequence and comparative analysis of human chromosome 5.";
Nature 431:268-274(2004).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L.,
Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R.,
Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V.,
Hannenhalli S., Turner R., Yooseph S., Lu F., Nusskern D.R.,
Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H.,
Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G.,
Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W.,
Venter J.C.;
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
TISSUE=Brain, Muscle, and Pancreas;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
FUNCTION, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=22241472; DOI=10.1074/jbc.M111.323485;
Veiga-da-Cunha M., Hadi F., Balligand T., Stroobant V.,
Van Schaftingen E.;
"Molecular identification of hydroxylysine kinase and of
ammoniophospholyases acting on 5-phosphohydroxy-L-lysine and
phosphoethanolamine.";
J. Biol. Chem. 287:7246-7255(2012).
[7]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[8]
VARIANTS PHLU ARG-240 AND VAL-437.
PubMed=23242558; DOI=10.1007/s10545-012-9568-9;
Veiga-da-Cunha M., Verhoeven-Duif N.M., de Koning T.J., Duran M.,
Dorland B., Van Schaftingen E.;
"Mutations in the AGXT2L2 gene cause phosphohydroxylysinuria.";
J. Inherit. Metab. Dis. 36:961-966(2013).
-!- FUNCTION: Catalyzes the pyridoxal-phosphate-dependent breakdown of
5-phosphohydroxy-L-lysine, converting it to ammonia, inorganic
phosphate and 2-aminoadipate semialdehyde.
{ECO:0000269|PubMed:22241472}.
-!- CATALYTIC ACTIVITY: (5R)-5-phosphonooxy-L-lysine + H(2)O = (S)-2-
amino-6-oxohexanoate + NH(3) + phosphate.
-!- COFACTOR:
Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
Evidence={ECO:0000269|PubMed:22241472};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=16 uM for 5-phosphohydroxy-L-lysine (at 30 degrees Celsius)
{ECO:0000269|PubMed:22241472};
Vmax=256 nmol/min/mg enzyme {ECO:0000269|PubMed:22241472};
-!- SUBUNIT: Homotetramer. {ECO:0000250}.
-!- INTERACTION:
Self; NbExp=4; IntAct=EBI-751947, EBI-751947;
Q9NUX5:POT1; NbExp=2; IntAct=EBI-751947, EBI-752420;
O60763:USO1; NbExp=3; IntAct=EBI-751947, EBI-356164;
Q08AM6:VAC14; NbExp=3; IntAct=EBI-751947, EBI-2107455;
-!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q8IUZ5-1; Sequence=Displayed;
Name=2;
IsoId=Q8IUZ5-2; Sequence=VSP_025585;
Name=3;
IsoId=Q8IUZ5-3; Sequence=VSP_025584;
-!- DISEASE: Phosphohydroxylysinuria (PHLU) [MIM:615011]: A condition
characterized by elevated phosphohydroxylysine in the urine. There
is no clinical phenotype associated with this finding other than
the urinary metabolites. {ECO:0000269|PubMed:23242558}. Note=The
disease is caused by mutations affecting the gene represented in
this entry.
-!- SIMILARITY: Belongs to the class-III pyridoxal-phosphate-dependent
aminotransferase family. {ECO:0000305}.
-!- CAUTION: Does not seem to possess aminotransferase activity.
{ECO:0000305|PubMed:22241472}.
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EMBL; AF318375; AAL55882.1; -; mRNA.
EMBL; AK023470; BAG51198.1; -; mRNA.
EMBL; AK292061; BAF84750.1; -; mRNA.
EMBL; AC136601; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; AC136632; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471165; EAW53836.1; -; Genomic_DNA.
EMBL; CH471165; EAW53841.1; -; Genomic_DNA.
EMBL; BC008009; AAH08009.1; -; mRNA.
EMBL; BC037567; AAH37567.1; -; mRNA.
EMBL; BC110335; AAI10336.1; -; mRNA.
CCDS; CCDS4434.1; -. [Q8IUZ5-1]
RefSeq; NP_001265275.1; NM_001278346.1.
RefSeq; NP_699204.1; NM_153373.3. [Q8IUZ5-1]
UniGene; Hs.248746; -.
ProteinModelPortal; Q8IUZ5; -.
SMR; Q8IUZ5; -.
BioGrid; 124425; 8.
IntAct; Q8IUZ5; 5.
STRING; 9606.ENSP00000310978; -.
DrugBank; DB00160; L-Alanine.
DrugBank; DB00114; Pyridoxal Phosphate.
iPTMnet; Q8IUZ5; -.
PhosphoSitePlus; Q8IUZ5; -.
DMDM; 74750645; -.
EPD; Q8IUZ5; -.
MaxQB; Q8IUZ5; -.
PaxDb; Q8IUZ5; -.
PeptideAtlas; Q8IUZ5; -.
PRIDE; Q8IUZ5; -.
ProteomicsDB; 70633; -.
ProteomicsDB; 70634; -. [Q8IUZ5-2]
ProteomicsDB; 70635; -. [Q8IUZ5-3]
DNASU; 85007; -.
Ensembl; ENST00000308158; ENSP00000310978; ENSG00000175309. [Q8IUZ5-1]
GeneID; 85007; -.
KEGG; hsa:85007; -.
UCSC; uc003miz.5; human. [Q8IUZ5-1]
CTD; 85007; -.
DisGeNET; 85007; -.
EuPathDB; HostDB:ENSG00000175309.14; -.
GeneCards; PHYKPL; -.
H-InvDB; HIX0164247; -.
HGNC; HGNC:28249; PHYKPL.
HPA; HPA036461; -.
HPA; HPA063608; -.
MalaCards; PHYKPL; -.
MIM; 614683; gene.
MIM; 615011; phenotype.
neXtProt; NX_Q8IUZ5; -.
OpenTargets; ENSG00000175309; -.
PharmGKB; PA162376015; -.
eggNOG; KOG1403; Eukaryota.
eggNOG; COG0160; LUCA.
GeneTree; ENSGT00530000062907; -.
HOGENOM; HOG000020206; -.
HOVERGEN; HBG004196; -.
InParanoid; Q8IUZ5; -.
KO; K18202; -.
OMA; YKVISRA; -.
OrthoDB; EOG091G08ZM; -.
PhylomeDB; Q8IUZ5; -.
TreeFam; TF320468; -.
Reactome; R-HSA-1442490; Collagen degradation.
Reactome; R-HSA-71064; Lysine catabolism.
ChiTaRS; PHYKPL; human.
GenomeRNAi; 85007; -.
PRO; PR:Q8IUZ5; -.
Proteomes; UP000005640; Chromosome 5.
Bgee; ENSG00000175309; Expressed in 195 organ(s), highest expression level in left lobe of thyroid gland.
CleanEx; HS_AGXT2L2; -.
ExpressionAtlas; Q8IUZ5; baseline and differential.
Genevisible; Q8IUZ5; HS.
GO; GO:0005759; C:mitochondrial matrix; TAS:Reactome.
GO; GO:0005739; C:mitochondrion; IBA:GO_Central.
GO; GO:0008453; F:alanine-glyoxylate transaminase activity; IBA:GO_Central.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0016829; F:lyase activity; TAS:Reactome.
GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
GO; GO:0030574; P:collagen catabolic process; TAS:Reactome.
GO; GO:0006554; P:lysine catabolic process; TAS:Reactome.
CDD; cd00610; OAT_like; 1.
Gene3D; 3.40.640.10; -; 1.
Gene3D; 3.90.1150.10; -; 2.
InterPro; IPR005814; Aminotrans_3.
InterPro; IPR015424; PyrdxlP-dep_Trfase.
InterPro; IPR015422; PyrdxlP-dep_Trfase_dom1.
InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
Pfam; PF00202; Aminotran_3; 1.
PIRSF; PIRSF000521; Transaminase_4ab_Lys_Orn; 1.
SUPFAM; SSF53383; SSF53383; 1.
PROSITE; PS00600; AA_TRANSFER_CLASS_3; 1.
1: Evidence at protein level;
Alternative splicing; Complete proteome; Disease mutation; Lyase;
Mitochondrion; Polymorphism; Pyridoxal phosphate; Reference proteome.
CHAIN 1 450 5-phosphohydroxy-L-lysine phospho-lyase.
/FTId=PRO_0000287667.
MOD_RES 278 278 N6-(pyridoxal phosphate)lysine.
{ECO:0000250}.
VAR_SEQ 1 343 Missing (in isoform 2).
{ECO:0000303|PubMed:15498874}.
/FTId=VSP_025585.
VAR_SEQ 1 275 Missing (in isoform 3).
{ECO:0000303|PubMed:14702039,
ECO:0000303|PubMed:15489334}.
/FTId=VSP_025584.
VARIANT 126 126 H -> R (in dbSNP:rs7707147).
/FTId=VAR_048233.
VARIANT 240 240 G -> R (in PHLU; dbSNP:rs201105857).
{ECO:0000269|PubMed:23242558}.
/FTId=VAR_069543.
VARIANT 437 437 E -> V (in PHLU; dbSNP:rs142181517).
{ECO:0000269|PubMed:14702039,
ECO:0000269|PubMed:23242558}.
/FTId=VAR_069544.
SEQUENCE 450 AA; 49711 MW; 5EB28A6BDD44C429 CRC64;
MAADQRPKAD TLALRQRLIS SSCRLFFPED PVKIVRAQGQ YMYDEQGAEY IDCISNVAHV
GHCHPLVVQA AHEQNQVLNT NSRYLHDNIV DYAQRLSETL PEQLCVFYFL NSGSEANDLA
LRLARHYTGH QDVVVLDHAY HGHLSSLIDI SPYKFRNLDG QKEWVHVAPL PDTYRGPYRE
DHPNPAMAYA NEVKRVVSSA QEKGRKIAAF FAESLPSVGG QIIPPAGYFS QVAEHIRKAG
GVFVADEIQV GFGRVGKHFW AFQLQGKDFV PDIVTMGKSI GNGHPVACVA ATQPVARAFE
ATGVEYFNTF GGSPVSCAVG LAVLNVLEKE QLQDHATSVG SFLMQLLGQQ KIKHPIVGDV
RGVGLFIGVD LIKDEATRTP ATEEAAYLVS RLKENYVLLS TDGPGRNILK FKPPMCFSLD
NARQVVAKLD AILTDMEEKV RSCETLRLQP


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