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P74416

- GCSP_SYNY3

UniProt

P74416 - GCSP_SYNY3

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Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein.UniRule annotation

Catalytic activityi

Glycine + [glycine-cleavage complex H protein]-N(6)-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N(6)-dihydrolipoyl-L-lysine + CO2.UniRule annotation

Cofactori

pyridoxal 5'-phosphateUniRule annotation

GO - Molecular functioni

  1. glycine dehydrogenase (decarboxylating) activity Source: UniProtKB-EC
  2. pyridoxal phosphate binding Source: InterPro

GO - Biological processi

  1. glycine decarboxylation via glycine cleavage system Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Pyridoxal phosphate

Names & Taxonomyi

Protein namesi
Recommended name:
Glycine dehydrogenase (decarboxylating)UniRule annotation (EC:1.4.4.2UniRule annotation)
Alternative name(s):
Glycine cleavage system P-proteinUniRule annotation
Glycine decarboxylaseUniRule annotation
Glycine dehydrogenase (aminomethyl-transferring)UniRule annotation
Gene namesi
Name:gcvPUniRule annotation
Ordered Locus Names:slr0293
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 983983Glycine dehydrogenase (decarboxylating)PRO_0000166942Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei726 – 7261N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

The glycine cleavage system is composed of four proteins: P, T, L and H.UniRule annotation

Protein-protein interaction databases

IntActiP74416. 2 interactions.
STRINGi1148.slr0293.

Structurei

Secondary structure

1
983
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi16 – 2611Combined sources
Helixi33 – 375Combined sources
Helixi42 – 5211Combined sources
Helixi57 – 648Combined sources
Helixi67 – 693Combined sources
Helixi83 – 9412Combined sources
Helixi115 – 1206Combined sources
Turni121 – 1233Combined sources
Helixi125 – 1284Combined sources
Helixi136 – 1383Combined sources
Helixi140 – 15718Combined sources
Beta strandi160 – 1623Combined sources
Helixi169 – 18214Combined sources
Beta strandi190 – 1945Combined sources
Helixi199 – 20911Combined sources
Helixi210 – 2123Combined sources
Beta strandi215 – 2195Combined sources
Helixi221 – 2233Combined sources
Beta strandi230 – 2389Combined sources
Helixi248 – 2569Combined sources
Beta strandi260 – 2656Combined sources
Helixi269 – 2713Combined sources
Helixi276 – 2794Combined sources
Beta strandi282 – 2876Combined sources
Turni289 – 2924Combined sources
Helixi296 – 2983Combined sources
Beta strandi303 – 3075Combined sources
Helixi309 – 3146Combined sources
Beta strandi319 – 3257Combined sources
Beta strandi330 – 3356Combined sources
Helixi337 – 3393Combined sources
Helixi341 – 3444Combined sources
Helixi345 – 3473Combined sources
Helixi357 – 39539Combined sources
Beta strandi403 – 41210Combined sources
Turni415 – 4173Combined sources
Helixi418 – 42710Combined sources
Beta strandi439 – 4435Combined sources
Helixi450 – 46112Combined sources
Beta strandi463 – 4653Combined sources
Helixi471 – 4766Combined sources
Helixi483 – 4853Combined sources
Helixi495 – 4973Combined sources
Helixi503 – 51513Combined sources
Turni520 – 5223Combined sources
Turni528 – 5303Combined sources
Helixi537 – 5404Combined sources
Helixi541 – 5444Combined sources
Helixi546 – 5494Combined sources
Helixi557 – 5593Combined sources
Helixi561 – 57818Combined sources
Beta strandi581 – 5844Combined sources
Helixi590 – 60718Combined sources
Beta strandi615 – 6195Combined sources
Helixi625 – 6328Combined sources
Beta strandi636 – 6405Combined sources
Beta strandi646 – 6483Combined sources
Helixi650 – 65910Combined sources
Helixi661 – 6633Combined sources
Beta strandi664 – 6729Combined sources
Helixi682 – 69110Combined sources
Beta strandi695 – 7006Combined sources
Helixi703 – 7053Combined sources
Turni706 – 7094Combined sources
Helixi712 – 7143Combined sources
Beta strandi718 – 7225Combined sources
Turni724 – 7285Combined sources
Turni733 – 7353Combined sources
Beta strandi742 – 7443Combined sources
Helixi746 – 7494Combined sources
Beta strandi773 – 7764Combined sources
Helixi781 – 7833Combined sources
Helixi784 – 81734Combined sources
Turni818 – 8203Combined sources
Beta strandi823 – 8253Combined sources
Helixi828 – 8303Combined sources
Beta strandi836 – 8394Combined sources
Helixi841 – 8477Combined sources
Helixi851 – 86010Combined sources
Beta strandi867 – 8693Combined sources
Beta strandi875 – 8784Combined sources
Helixi886 – 90722Combined sources
Beta strandi913 – 9164Combined sources
Helixi917 – 9204Combined sources
Helixi925 – 9295Combined sources
Beta strandi935 – 9373Combined sources
Helixi939 – 9435Combined sources
Helixi947 – 9504Combined sources
Helixi963 – 9686Combined sources
Beta strandi970 – 9723Combined sources
Helixi974 – 9763Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4LGLX-ray2.00A/B1-983[»]
4LHCX-ray1.90A/B1-983[»]
4LHDX-ray1.80A/B1-983[»]
ProteinModelPortaliP74416.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.UniRule annotation

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239369.
InParanoidiP74416.
KOiK00281.
OMAiFDSRPYS.
OrthoDBiEOG6HMXDX.
PhylomeDBiP74416.

Family and domain databases

Gene3Di3.40.640.10. 2 hits.
HAMAPiMF_00711. GcvP.
InterProiIPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR003437. GDC_P_homo.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PANTHERiPTHR11773. PTHR11773. 1 hit.
PfamiPF02347. GDC-P. 2 hits.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 3 hits.
TIGRFAMsiTIGR00461. gcvP. 1 hit.

Sequencei

Sequence statusi: Complete.

P74416-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPNLEPAVVV PTSEAIAVDL TKLEEKLAPA DSFLDRHLGP GETEQRQMLQ
60 70 80 90 100
TLGFDTLGDL IDQAVPPAIR FPRSLQLPAS QSEYGAIAQL KSIASKNQVF
110 120 130 140 150
RSYIGMGYYD TITPPVIQRN ILENPGWYTA YTPYQAEIAQ GRLEALLNFQ
160 170 180 190 200
TMVMDLTGLE IANASLLDEG TAAAEAMALS YGVSKSKANA FFVAQDCHPQ
210 220 230 240 250
TIEVIKTRAN PLGIEVIVGD HHTFSFSTSI FGALLQYPAT DGAVYDYRSF
260 270 280 290 300
IDKAHQHQAL VTLAADPLSL TLLTPPGELG ADIAVGSTQR FGIPLGYGGP
310 320 330 340 350
HAAYFATKAE YQRKMPGRIV GVSKDAHGNP ALRLALQTRE QHIRRDKATS
360 370 380 390 400
NICTAQVLLA VMASMYGVYH GSTGLKNIAL RIHQLTVLLA IGLKRLNYSL
410 420 430 440 450
NNDYFFDTLR VGVGEQSAPA ILKAAEGRGI NLRPLVPGEV GISLDETVTV
460 470 480 490 500
QDLLDLWQVF AGKDNLPFTP EELWSEVKTS FPADLTRQSL YLQDAVFNQY
510 520 530 540 550
HSETELLRYL HQLESKDLAL NTSMIPLGSC TMKLNATAEM MPVTWPEFGK
560 570 580 590 600
IHPFAPAGQT EGYQILFAQL EAWLGEITGF DAISLQPNAG SQGEYAGLQV
610 620 630 640 650
IRQYHLSRGE EQRNICLIPE SAHGTNPASA VMCGMQVVPV KCDGEGNIDV
660 670 680 690 700
EDLTSKAEKY GDRLAALMVT YPSTHGVFEA TIGTICDIVH RFGGEVYMDG
710 720 730 740 750
ANMNAQVGLC RPADFGADVC HLNLHKTFCI PHGGGGPGMG PIGVKSHLQA
760 770 780 790 800
FLPRTSLNST AELQAEDQSI GMISAAPYGS ASILVISWMY IAMMGPQGLT
810 820 830 840 850
KATEVAILSA NYMAKRLENY YPILFRGNNE LVAHECILDL RPLKKQAAIE
860 870 880 890 900
VEDVAKRLMD FGFHAPTVSW PVLGTMMVEP TESESLGELD RFCDAMIAIY
910 920 930 940 950
QEAQAITHGE IDPADNPLKN APHTAQSLIC GEWNHPYSQE EAAYPAPWTK
960 970 980
QFKFWPAVGR INNTYGDRHL VCSCEGMEAY KEG
Length:983
Mass (Da):107,322
Last modified:February 1, 1997 - v1
Checksum:i4009367B62A2936F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA18516.1.
PIRiS76257.
RefSeqiNP_441838.1. NC_000911.1.
YP_005651898.1. NC_017277.1.
YP_007451719.1. NC_020286.1.

Genome annotation databases

EnsemblBacteriaiBAA18516; BAA18516; BAA18516.
GeneIDi952059.
KEGGisyn:slr0293.
PATRICi23841192. VBISynSp132158_2147.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA18516.1 .
PIRi S76257.
RefSeqi NP_441838.1. NC_000911.1.
YP_005651898.1. NC_017277.1.
YP_007451719.1. NC_020286.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4LGL X-ray 2.00 A/B 1-983 [» ]
4LHC X-ray 1.90 A/B 1-983 [» ]
4LHD X-ray 1.80 A/B 1-983 [» ]
ProteinModelPortali P74416.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P74416. 2 interactions.
STRINGi 1148.slr0293.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAA18516 ; BAA18516 ; BAA18516 .
GeneIDi 952059.
KEGGi syn:slr0293.
PATRICi 23841192. VBISynSp132158_2147.

Phylogenomic databases

eggNOGi COG1003.
HOGENOMi HOG000239369.
InParanoidi P74416.
KOi K00281.
OMAi FDSRPYS.
OrthoDBi EOG6HMXDX.
PhylomeDBi P74416.

Family and domain databases

Gene3Di 3.40.640.10. 2 hits.
HAMAPi MF_00711. GcvP.
InterProi IPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR003437. GDC_P_homo.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view ]
PANTHERi PTHR11773. PTHR11773. 1 hit.
Pfami PF02347. GDC-P. 2 hits.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 3 hits.
TIGRFAMsi TIGR00461. gcvP. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 6803 / Kazusa.

Entry informationi

Entry nameiGCSP_SYNY3
AccessioniPrimary (citable) accession number: P74416
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2003
Last sequence update: February 1, 1997
Last modified: November 26, 2014
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

External Data

Dasty 3