Q54089 (RELA_STREQ) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional (p)ppGpp synthase/hydrolase RelA

Including the following 2 domains:

1. GTP pyrophosphokinase
   EC=2.7.6.5
   Alternative name(s):
   (p)ppGpp synthase
   ATP:GTP 3'-pyrophosphotransferase
   Stringent response-like protein
   ppGpp synthase I
2. Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase
   EC=3.1.7.2
   Alternative name(s):
   Penta-phosphate guanosine-3'-pyrophosphohydrolase
   Short name=(ppGpp)ase

Gene names

Name:	relA
Synonyms:	rel

Organism

Streptococcus dysgalactiae subsp. equisimilis (Streptococcus equisimilis)

Taxonomic identifier

119602 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Lactobacillales › Streptococcaceae › Streptococcus › Streptococcus dysgalactiae group › Streptococcus dysgalactiae

Protein attributes

Sequence length	739 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance. This enzyme catalyzes both the formation of pppGpp which is then hydrolyzed to form ppGpp, and the hydrolysis of ppGpp. The enzyme does not simultaneously display both synthase and hydrolase activities. In the structure of residues 1-385 there are 2 conformations seen, the hydrolase-OFF/synthase-ON and hydrolase-ON/synthase-OFF, suggesting there is ligand-induced signal transmission between the 2 active sites.
Catalytic activity	ATP + GTP = AMP + guanosine 3'-diphosphate 5'-triphosphate. Guanosine 3',5'-bis(diphosphate) + H2O = guanosine 5'-diphosphate + diphosphate.
Cofactor	Binds 1 Mg2+ per subunit Potential. Ref.3 Binds 1 Mn2+ per subunit. Ref.3
Enzyme regulation	Alpha-beta methylenyl ATP, an ATP-analog inhibitor of the synthase activity also reduces the hydrolase activity about 4-fold. Ref.2 Ref.3
Pathway	Purine metabolism; ppGpp biosynthesis; ppGpp from GDP: step 1/1. Purine metabolism; ppGpp biosynthesis; ppGpp from GTP: step 1/2.
Domain	Based on a random mutagenesis study of the catalytic fragment (residues 1-385), the (p)ppGpp phosphohydrolase domain seems to encompass approximately the first 225 residues, while the (p)ppGpp synthase domain seems to be found between residues 226 and 385.
Sequence similarities	Belongs to the RelA/SpoT family. Contains 1 ACT domain. Contains 1 HD domain.
Biophysicochemical properties	Kinetic parameters: KM=2 mM for GTP Ref.2 KM=5 mM for ATP

Ontologies

Keywords
Ligand	ATP-binding GTP-binding Magnesium Manganese Metal-binding Nucleotide-binding
Molecular function	Hydrolase Kinase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	guanosine tetraphosphate biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP binding Inferred from electronic annotation. Source: UniProtKB-KW GTP diphosphokinase activity Inferred from electronic annotation. Source: EC amino acid binding Inferred from electronic annotation. Source: InterPro guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity Inferred from electronic annotation. Source: EC kinase activity Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoric diester hydrolase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 739

739

Bifunctional (p)ppGpp synthase/hydrolase RelA

PRO_0000166565

Regions

Domain

50 – 149

100

HD

Domain

663 – 737

75

ACT

Sites

Active site

81

1

Nucleophile, for hydrolase activity Potential

Active site

82

1

Nucleophile, for hydrolase activity Potential

Metal binding

53

1

Manganese

Metal binding

77

1

Manganese

Metal binding

144

1

Manganese

Metal binding

264

1

Magnesium Potential

Experimental info

Mutagenesis

44

1

R → Q: No hydrolase activity. Ref.3

Mutagenesis

78

1

D → A: No hydrolase activity. Ref.3

Mutagenesis

81

1

E → G: No hydrolase activity. Ref.3

Mutagenesis

82

1

D → V: No hydrolase activity. Ref.3

Mutagenesis

151

1

T → A or P: No hydrolase activity. Ref.3

Mutagenesis

264

1

D → G: No synthase activity. Ref.3

Mutagenesis

323

1

E → Q: No synthase activity. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

739

Helix Strand Turn

Details...

Helix

9 – 19

11

Helix

22 – 38

17

Turn

39 – 41

3

Helix

52 – 63

12

Helix

68 – 76

9

Helix

79 – 82

4

Helix

87 – 94

8

Helix

96 – 108

13

Turn

128 – 130

3

Helix

135 – 150

16

Helix

160 – 169

10

Helix

171 – 177

7

Helix

181 – 195

15

Helix

197 – 209

13

Helix

211 – 230

20

Turn

231 – 233

3

Beta strand

237 – 240

4

Helix

245 – 255

11

Helix

256 – 258

3

Helix

263 – 265

3

Beta strand

267 – 274

8

Helix

275 – 288

14

Turn

299 – 301

3

Beta strand

311 – 316

6

Beta strand

318 – 328

11

Helix

329 – 337

9

Helix

364 – 370

7

Sequences

	Sequence		Length	Mass (Da)
	Q54089 [UniParc]. Last modified November 1, 1997. Version 1. Checksum: E65CBEF99103D171	FASTA	739	83,913
	10 20 30 40 50 60 MAKEINLTGE EVVALAAKYM NETDAAFVKK ALDYATAAHF YQVRKSGEPY IVHPIQVAGI 70 80 90 100 110 120 LADLHLDAVT VACGFLHDVV EDTDITLDNI EFDFGKDVRD IVDGVTKLGK VEYKSHEEQL 130 140 150 160 170 180 AENHRKMLMA MSKDIRVILV KLADRLHNMR TLKHLRKDKQ ERISRETMEI YAPLAHRLGI 190 200 210 220 230 240 SRIKWELEDL AFRYLNETEF YKISHMMNEK RREREALVDD IVTKIKSYTT EQGLFGDVYG 250 260 270 280 290 300 RPKHIYSIYR KMRDKKKRFD QIFDLIAIRC VMETQSDVYA MVGYIHELWR PMPGRFKDYI 310 320 330 340 350 360 AAPKANGYQS IHTTVYGPKG PIEIQIRTKE MHQVAEYGVA AHWAYKKGVR GKVNQAEQKV 370 380 390 400 410 420 GMNWIKELVE LQDASNGDAV DFVDSVKEDI FSERIYVFTP TGAVQELPKD SGPIDFAYAI 430 440 450 460 470 480 HTQVGEKAIG AKVNGRMVPL TAKLKTGDVV EIVTNPNSFG PSRDWIKLVK TNKARNKIRQ 490 500 510 520 530 540 FFKNQDKELS VNKGRDMLVS YFQEQGYVAN KYLDKKRIEA ILPKVSVKSE ESLYAAVGFG 550 560 570 580 590 600 DISPVSVFNK LTEKERREEE RAKAKAEAEE LVNGGEIKHE NKDVLKVRSE NGVIIQGASG 610 620 630 640 650 660 LLMRIAKCCN PVPGDPIEGY ITKGRGIAIH RADCNNIKSQ DGYQERLIEV EWDLDNSSKD 670 680 690 700 710 720 YQAEIDIYGL NRRGLLNDVL QILSNSTKSI STVNAQPTKD MKFANIHVSF GIPNLTHLTT 730 VVEKIKAVPD VYSVKRTNG

References

[1]	"Genetic organization of the streptokinase region of the Streptococcus equisimilis H46A chromosome." Mechold U., Steiner K., Vettermann S., Malke H. Mol. Gen. Genet. 241:129-140(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: H46A.
[2]	"Intramolecular regulation of the opposing (p)ppGpp catalytic activities of Rel(Seq), the Rel/Spo enzyme from Streptococcus equisimilis." Mechold U., Murphy H., Brown L., Cashel M. J. Bacteriol. 184:2878-2888(2002) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[3]	"Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response." Hogg T., Mechold U., Malke H., Cashel M., Hilgenfeld R. Cell 117:57-68(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-385 BOUND TO GUANOSINE-NUCLEOTIDE DERIVATIVES, HYDROLASE AND SYNTHASE ACTIVITIES, COFACTOR, ENZYME REGULATION, MUTAGENESIS OF ARG-44; ASP-78; GLU-81; ASP-82; THR-151; ASP-264 AND GLU-323. Strain: H46A.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X72832 Genomic DNA. Translation: CAA51353.1.

PIR

S39975.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1VJ7	X-ray	2.10	A/B	1-385	[»]

ProteinModelPortal

Q54089.

SMR

Q54089. Positions 5-371.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

Q54089.

UniPathway

UPA00908; UER00884.
UPA00908; UER00886.

Family and domain databases

Gene3D

3.10.20.30. 1 hit.

InterPro

IPR026020. (p)ppGpp_Synthase.
IPR002912. ACT_dom.
IPR012675. Beta-grasp_dom.
IPR003607. HD/PDEase_dom.
IPR006674. HD_domain.
IPR004811. RelA/Spo_fam.
IPR007685. RelA_SpoT.
IPR004095. TGS.
IPR012676. TGS-like.
[Graphical view]

PANTHER

PTHR21262. PTHR21262. 1 hit.

Pfam

PF01842. ACT. 1 hit.
PF01966. HD. 1 hit.
PF04607. RelA_SpoT. 1 hit.
PF02824. TGS. 1 hit.
[Graphical view]

SMART

SM00471. HDc. 1 hit.
SM00954. RelA_SpoT. 1 hit.
[Graphical view]

SUPFAM

SSF81271. TGS-like. 1 hit.

TIGRFAMs

TIGR00691. spoT_relA. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1163118.

EvolutionaryTrace

Q54089.

Entry information

Entry name

RELA_STREQ

Accession

Primary (citable) accession number: Q54089

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	April 3, 2013
This is version 85 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program