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Q5SKW7

- GCSPB_THET8

UniProt

Q5SKW7 - GCSPB_THET8

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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: 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 phosphate.UniRule 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

Enzyme and pathway databases

BioCyciTTHE300852:GH8R-551-MONOMER.

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
ProteomesiUP000000532: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 474474Probable glycine dehydrogenase (decarboxylating) subunit 2PRO_1000045709Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei266 – 2661N6-(pyridoxal phosphate)lysineUniRule annotation

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

1
474
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 94
Helixi26 – 294
Helixi32 – 343
Helixi47 – 5812
Turni64 – 663
Turni72 – 743
Helixi81 – 888
Helixi99 – 1013
Helixi103 – 12018
Beta strandi123 – 1264
Helixi132 – 14918
Turni153 – 1553
Beta strandi158 – 1625
Helixi168 – 1758
Beta strandi179 – 1835
Beta strandi189 – 1913
Helixi193 – 1997
Beta strandi204 – 2096
Helixi222 – 23110
Beta strandi235 – 2395
Helixi240 – 2456
Turni246 – 2494
Helixi252 – 2554
Beta strandi258 – 2614
Turni264 – 2685
Helixi273 – 2753
Beta strandi282 – 2843
Helixi286 – 2916
Beta strandi296 – 2994
Beta strandi304 – 3074
Beta strandi317 – 3193
Helixi324 – 36239
Beta strandi377 – 3804
Helixi387 – 39610
Beta strandi403 – 4053
Beta strandi414 – 4163
Helixi424 – 43815
Helixi442 – 4465
Beta strandi451 – 4544
Helixi459 – 4646
Beta strandi469 – 4713

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1WYTX-ray2.40B/D1-474[»]
1WYUX-ray2.10B/D/F/H1-474[»]
1WYVX-ray2.40B/D/F/H1-474[»]
ProteinModelPortaliQ5SKW7.
SMRiQ5SKW7. Positions 2-474.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5SKW7.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1003.
HOGENOMiHOG000239368.
KOiK00283.
OMAiWTGLMMI.
OrthoDBiEOG6HMXDX.
PhylomeDBiQ5SKW7.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
HAMAPiMF_00713. GcvPB.
InterProiIPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR023012. GDC_P_su2.
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:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AP008226 Genomic DNA. Translation: BAD70349.1 .
RefSeqi WP_011228003.1. NC_006461.1.
YP_143792.1. NC_006461.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1WYT X-ray 2.40 B/D 1-474 [» ]
1WYU X-ray 2.10 B/D/F/H 1-474 [» ]
1WYV X-ray 2.40 B/D/F/H 1-474 [» ]
ProteinModelPortali Q5SKW7.
SMRi Q5SKW7. Positions 2-474.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 300852.TTHA0526.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai BAD70349 ; BAD70349 ; BAD70349 .
GeneIDi 3168946.
KEGGi ttj:TTHA0526.
PATRICi 23956027. VBITheThe93045_0524.

Phylogenomic databases

eggNOGi COG1003.
HOGENOMi HOG000239368.
KOi K00283.
OMAi WTGLMMI.
OrthoDBi EOG6HMXDX.
PhylomeDBi Q5SKW7.

Enzyme and pathway databases

BioCyci TTHE300852:GH8R-551-MONOMER.

Miscellaneous databases

EvolutionaryTracei Q5SKW7.

Family and domain databases

Gene3Di 3.40.640.10. 1 hit.
HAMAPi MF_00713. GcvPB.
InterProi IPR020580. GDC-P_N.
IPR020581. GDC_P.
IPR023012. GDC_P_su2.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
[Graphical view ]
PANTHERi PTHR11773. PTHR11773. 1 hit.
Pfami PF02347. GDC-P. 1 hit.
[Graphical view ]
SUPFAMi SSF53383. SSF53383. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Complete genome sequence of Thermus thermophilus HB8."
    Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T., Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.
    Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HB8 / ATCC 27634 / DSM 579.
  2. "Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia."
    Nakai T., Nakagawa N., Maoka N., Masui R., Kuramitsu S., Kamiya N.
    EMBO J. 24:1523-1536(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS).

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: October 1, 2014
This is version 68 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

External Data

Dasty 3