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Protein

Probable glycine dehydrogenase (decarboxylating) subunit 2

Gene

gcvPB

Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
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

Names & Taxonomyi

Protein namesi
Recommended name:
Probable glycine dehydrogenase (decarboxylating) subunit 2UniRule annotation (EC:1.4.4.2UniRule annotation)
Alternative name(s):
Glycine cleavage system P-protein subunit 2UniRule annotation
Glycine decarboxylase subunit 2UniRule annotation
Glycine dehydrogenase (aminomethyl-transferring) subunit 2UniRule annotation
Gene namesi
Name:gcvPBUniRule annotation
Ordered Locus Names:TTHA0526
OrganismiThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Taxonomic identifieri300852 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000532 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000457091 – 474Probable glycine dehydrogenase (decarboxylating) subunit 2Add BLAST474

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei266N6-(pyridoxal phosphate)lysineUniRule annotation1

Proteomic databases

PRIDEiQ5SKW7.

Interactioni

Subunit structurei

The glycine cleavage system is composed of four proteins: P, T, L and H. In this organism, the P 'protein' is a heterodimer of two subunits.UniRule annotation

Protein-protein interaction databases

STRINGi300852.TTHA0526.

Structurei

Secondary structure

1474
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 9Combined sources4
Helixi26 – 29Combined sources4
Helixi32 – 34Combined sources3
Helixi47 – 58Combined sources12
Turni64 – 66Combined sources3
Turni72 – 74Combined sources3
Helixi81 – 88Combined sources8
Helixi99 – 101Combined sources3
Helixi103 – 120Combined sources18
Beta strandi123 – 126Combined sources4
Helixi132 – 149Combined sources18
Turni153 – 155Combined sources3
Beta strandi158 – 162Combined sources5
Helixi168 – 175Combined sources8
Beta strandi179 – 183Combined sources5
Beta strandi189 – 191Combined sources3
Helixi193 – 199Combined sources7
Beta strandi204 – 209Combined sources6
Helixi222 – 231Combined sources10
Beta strandi235 – 239Combined sources5
Helixi240 – 245Combined sources6
Turni246 – 249Combined sources4
Helixi252 – 255Combined sources4
Beta strandi258 – 261Combined sources4
Turni264 – 268Combined sources5
Helixi273 – 275Combined sources3
Beta strandi282 – 284Combined sources3
Helixi286 – 291Combined sources6
Beta strandi296 – 299Combined sources4
Beta strandi304 – 307Combined sources4
Beta strandi317 – 319Combined sources3
Helixi324 – 362Combined sources39
Beta strandi377 – 380Combined sources4
Helixi387 – 396Combined sources10
Beta strandi403 – 405Combined sources3
Beta strandi414 – 416Combined sources3
Helixi424 – 438Combined sources15
Helixi442 – 446Combined sources5
Beta strandi451 – 454Combined sources4
Helixi459 – 464Combined sources6
Beta strandi469 – 471Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WYTX-ray2.40B/D1-474[»]
1WYUX-ray2.10B/D/F/H1-474[»]
1WYVX-ray2.40B/D/F/H1-474[»]
ProteinModelPortaliQ5SKW7.
SMRiQ5SKW7.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SKW7.

Family & Domainsi

Sequence similaritiesi

Belongs to the GcvP family. C-terminal subunit subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CBI. Bacteria.
COG1003. LUCA.
HOGENOMiHOG000239368.
KOiK00283.
OMAiMHINLHK.
PhylomeDBiQ5SKW7.

Family and domain databases

CDDicd00613. GDC-P. 1 hit.
Gene3Di3.40.640.10. 1 hit.
HAMAPiMF_00713. GcvPB. 1 hit.
InterProiIPR023012. GcvPB.
IPR020581. GDC_P.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PANTHERiPTHR11773. PTHR11773. 1 hit.
PfamiPF02347. GDC-P. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.

Sequencei

Sequence statusi: Complete.

Q5SKW7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFPLIFERS RKGRRGLKLV KAVPKAEDLI PKEHLREVPP RLPEVDELTL
60 70 80 90 100
VRHYTGLSRR QVGVDTTFYP LGSCTMKYNP KLHEEAARLF ADLHPYQDPR
110 120 130 140 150
TAQGALRLMW ELGEYLKALT GMDAITLEPA AGAHGELTGI LIIRAYHEDR
160 170 180 190 200
GEGRTRRVVL VPDSAHGSNP ATASMAGYQV REIPSGPEGE VDLEALKREL
210 220 230 240 250
GPHVAALMLT NPNTLGLFER RILEISRLCK EAGVQLYYDG ANLNAIMGWA
260 270 280 290 300
RPGDMGFDVV HLNLHKTFTV PHGGGGPGSG PVGVKAHLAP YLPVPLVERG
310 320 330 340 350
EEGFYLDFDR PKSIGRVRSF YGNFLALVRA WAYIRTLGLE GLKKAAALAV
360 370 380 390 400
LNARYLKELL KEKGYRVPYD GPSMHEFVAQ PPEGFRALDL AKGLLELGFH
410 420 430 440 450
PPTVYFPLIV KEALMVEPTE TEAKETLEAF AEAMGALLKK PKEWLENAPY
460 470
STPVRRLDEL RANKHPKLTY FDEG
Length:474
Mass (Da):52,709
Last modified:December 21, 2004 - v1
Checksum:iA8B48175AF156C1D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70349.1.
RefSeqiWP_011228003.1. NC_006461.1.
YP_143792.1. NC_006461.1.

Genome annotation databases

EnsemblBacteriaiBAD70349; BAD70349; BAD70349.
GeneIDi3168946.
KEGGittj:TTHA0526.
PATRICi23956027. VBITheThe93045_0524.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP008226 Genomic DNA. Translation: BAD70349.1.
RefSeqiWP_011228003.1. NC_006461.1.
YP_143792.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WYTX-ray2.40B/D1-474[»]
1WYUX-ray2.10B/D/F/H1-474[»]
1WYVX-ray2.40B/D/F/H1-474[»]
ProteinModelPortaliQ5SKW7.
SMRiQ5SKW7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi300852.TTHA0526.

Proteomic databases

PRIDEiQ5SKW7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD70349; BAD70349; BAD70349.
GeneIDi3168946.
KEGGittj:TTHA0526.
PATRICi23956027. VBITheThe93045_0524.

Phylogenomic databases

eggNOGiENOG4105CBI. Bacteria.
COG1003. LUCA.
HOGENOMiHOG000239368.
KOiK00283.
OMAiMHINLHK.
PhylomeDBiQ5SKW7.

Miscellaneous databases

EvolutionaryTraceiQ5SKW7.

Family and domain databases

CDDicd00613. GDC-P. 1 hit.
Gene3Di3.40.640.10. 1 hit.
HAMAPiMF_00713. GcvPB. 1 hit.
InterProiIPR023012. GcvPB.
IPR020581. GDC_P.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view]
PANTHERiPTHR11773. PTHR11773. 1 hit.
PfamiPF02347. GDC-P. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiGCSPB_THET8
AccessioniPrimary (citable) accession number: Q5SKW7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: December 21, 2004
Last modified: November 2, 2016
This is version 79 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

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.