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Protein

Glycine dehydrogenase (decarboxylating)

Gene

gcvP

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed-Annotation score: 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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi1.4.4.2. 382.

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 lineageiBacteriaCyanobacteriaSynechococcalesMerismopediaceaeSynechocystis
Proteomesi
  • UP000001425 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001669421 – 983Glycine dehydrogenase (decarboxylating)Add BLAST983

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei726N6-(pyridoxal phosphate)lysineUniRule annotation1

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 interactors.

Structurei

Secondary structure

1983
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi16 – 26Combined sources11
Helixi33 – 37Combined sources5
Helixi42 – 52Combined sources11
Helixi57 – 64Combined sources8
Helixi67 – 69Combined sources3
Helixi83 – 94Combined sources12
Helixi115 – 120Combined sources6
Turni121 – 123Combined sources3
Helixi125 – 128Combined sources4
Helixi136 – 138Combined sources3
Helixi140 – 157Combined sources18
Beta strandi160 – 162Combined sources3
Helixi169 – 182Combined sources14
Beta strandi190 – 194Combined sources5
Helixi199 – 209Combined sources11
Helixi210 – 212Combined sources3
Beta strandi215 – 219Combined sources5
Helixi221 – 223Combined sources3
Beta strandi230 – 238Combined sources9
Helixi248 – 256Combined sources9
Beta strandi260 – 265Combined sources6
Helixi269 – 271Combined sources3
Helixi276 – 279Combined sources4
Beta strandi282 – 287Combined sources6
Turni289 – 292Combined sources4
Helixi296 – 298Combined sources3
Beta strandi303 – 307Combined sources5
Helixi309 – 314Combined sources6
Beta strandi319 – 325Combined sources7
Beta strandi330 – 335Combined sources6
Helixi337 – 339Combined sources3
Helixi341 – 344Combined sources4
Helixi345 – 347Combined sources3
Helixi357 – 395Combined sources39
Beta strandi403 – 412Combined sources10
Turni415 – 417Combined sources3
Helixi418 – 427Combined sources10
Beta strandi439 – 443Combined sources5
Helixi450 – 461Combined sources12
Beta strandi463 – 465Combined sources3
Helixi471 – 476Combined sources6
Helixi483 – 485Combined sources3
Helixi495 – 497Combined sources3
Helixi503 – 515Combined sources13
Turni520 – 522Combined sources3
Turni528 – 530Combined sources3
Helixi537 – 540Combined sources4
Helixi541 – 544Combined sources4
Helixi546 – 549Combined sources4
Helixi557 – 559Combined sources3
Helixi561 – 578Combined sources18
Beta strandi581 – 584Combined sources4
Helixi590 – 607Combined sources18
Beta strandi615 – 619Combined sources5
Helixi625 – 632Combined sources8
Beta strandi636 – 640Combined sources5
Beta strandi646 – 648Combined sources3
Helixi650 – 659Combined sources10
Helixi661 – 663Combined sources3
Beta strandi664 – 672Combined sources9
Helixi682 – 691Combined sources10
Beta strandi695 – 700Combined sources6
Helixi703 – 705Combined sources3
Turni706 – 709Combined sources4
Helixi712 – 714Combined sources3
Beta strandi718 – 722Combined sources5
Turni724 – 728Combined sources5
Turni733 – 735Combined sources3
Beta strandi742 – 744Combined sources3
Helixi746 – 749Combined sources4
Beta strandi773 – 776Combined sources4
Helixi781 – 783Combined sources3
Helixi784 – 817Combined sources34
Turni818 – 820Combined sources3
Beta strandi823 – 825Combined sources3
Helixi828 – 830Combined sources3
Beta strandi836 – 839Combined sources4
Helixi841 – 847Combined sources7
Helixi851 – 860Combined sources10
Beta strandi867 – 869Combined sources3
Beta strandi875 – 878Combined sources4
Helixi886 – 907Combined sources22
Beta strandi913 – 916Combined sources4
Helixi917 – 920Combined sources4
Helixi925 – 929Combined sources5
Beta strandi935 – 937Combined sources3
Helixi939 – 943Combined sources5
Helixi947 – 950Combined sources4
Helixi963 – 968Combined sources6
Beta strandi970 – 972Combined sources3
Helixi974 – 976Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LGLX-ray2.00A/B1-983[»]
4LHCX-ray1.90A/B1-983[»]
4LHDX-ray1.80A/B1-983[»]
ProteinModelPortaliP74416.
SMRiP74416.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000239369.
InParanoidiP74416.
KOiK00281.
OMAiCVPMSEY.
PhylomeDBiP74416.

Family and domain databases

CDDicd00613. GDC-P. 2 hits.
Gene3Di3.40.640.10. 2 hits.
HAMAPiMF_00711. GcvP. 1 hit.
InterProiIPR003437. GcvP.
IPR020581. GDC_P.
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.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA18516.1.
PIRiS76257.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LGLX-ray2.00A/B1-983[»]
4LHCX-ray1.90A/B1-983[»]
4LHDX-ray1.80A/B1-983[»]
ProteinModelPortaliP74416.
SMRiP74416.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP74416. 2 interactors.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

HOGENOMiHOG000239369.
InParanoidiP74416.
KOiK00281.
OMAiCVPMSEY.
PhylomeDBiP74416.

Enzyme and pathway databases

BRENDAi1.4.4.2. 382.

Family and domain databases

CDDicd00613. GDC-P. 2 hits.
Gene3Di3.40.640.10. 2 hits.
HAMAPiMF_00711. GcvP. 1 hit.
InterProiIPR003437. GcvP.
IPR020581. GDC_P.
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.
ProtoNetiSearch...

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 2, 2016
This is version 102 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

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.