P18314 (URE1_ENTAE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Urease subunit alpha
EC=3.5.1.5

Alternative name(s):
Urea amidohydrolase subunit alpha

Gene names

Name:

ureC

Organism

Enterobacter aerogenes (Aerobacter aerogenes)

Taxonomic identifier

548 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Enterobacter

Protein attributes

Sequence length	567 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	Urea + H2O = CO2 + 2 NH3. Ref.1 Ref.3 Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.10
Cofactor	Binds 2 nickel ions per subunit. Ref.2 Ref.3 Ref.4
Enzyme regulation	The apoenzyme can be activated in vitro in the presence of nickel ions and carbon dioxide, which promotes carbamylation of Lys-217. Ref.7 Ref.8 Ref.9 Ref.10
Pathway	Nitrogen metabolism; urea degradation; CO(2) and NH(3) from urea (urease route): step 1/1. HAMAP-Rule MF_01953
Subunit structure	Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. The apoenzyme interacts with an accessory complex composed of UreD, UreF and UreG, which is required for the assembly of the nickel containing metallocenter of UreC. The UreE protein may also play a direct role as a metallochaperone in nickel transfer to the urease apoprotein. Ref.5 Ref.6 Ref.8 Ref.9 Ref.12
Subcellular location	Cytoplasm By similarity HAMAP-Rule MF_01953.
Post-translational modification	Carbamylation allows a single lysine to coordinate two nickel ions. HAMAP-Rule MF_01953
Sequence similarities	Belongs to the urease family. Contains 1 urease domain.
Biophysicochemical properties	Kinetic parameters: KM=2.3 mM for urea Ref.3 Ref.4 Ref.11 Ref.19 Vmax=1.9 mmol/min/mg enzyme pH dependence: Optimum pH is 7.75.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Metal-binding Nickel
Molecular function	Hydrolase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	urea catabolic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	nickel cation binding Inferred from electronic annotation. Source: HAMAP urease activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ureA	P18316	11	EBI-1028571,EBI-1028581

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 567

567

Urease subunit alpha HAMAP-Rule MF_01953

PRO_0000067543

Regions

Domain

129 – 567

439

Urease

Sites

Active site

320

1

Proton donor

Metal binding

134

1

Nickel 2

Metal binding

136

1

Nickel 2

Metal binding

217

1

Nickel 1; via carbamate group

Metal binding

217

1

Nickel 2; via carbamate group

Metal binding

246

1

Nickel 1

Metal binding

272

1

Nickel 1

Metal binding

360

1

Nickel 2

Binding site

219

1

Substrate

Amino acid modifications

Modified residue

217

1

N6-carboxylysine HAMAP-Rule MF_01953

Experimental info

Mutagenesis

134

1

H → A: Abrogates activity and reduces binding to nickel ions. Ref.4

Mutagenesis

136

1

H → A: Abrogates activity and reduces binding to nickel ions. Ref.4

Mutagenesis

217

1

K → A, C or E: Reduces activity 8000-fold and abrogates binding to nickel ions. Ref.17

Mutagenesis

219

1

H → A: Reduces activity 500-fold and increases KM 1000-fold. Resistant to inactivation by diethylpyrocarbonate and iodoacetamide. Ref.4 Ref.19

Mutagenesis

219

1

H → N or Q: Increases KM 100-fold; optimum pH is 6. Ref.4 Ref.19

Mutagenesis

221

1

D → A: Reduces activity 1000-fold and increases KM 10-fold. Ref.19

Mutagenesis

221

1

D → N: Reduces activity 50-fold. Ref.19

Mutagenesis

246

1

H → A: Abrogates activity and reduces binding to nickel ions. Ref.4

Mutagenesis

312

1

H → A: Enhances thermal stability above 50 degrees Celsius.

Mutagenesis

319

1

C → A: Reduces activity 2-fold, but increases KM only 1.7-fold; optimum pH is 6.7. Reduces binding of nickel ions. Resistant to inactivation by iodoacetamide. Ref.3 Ref.18

Mutagenesis

319

1

C → D: Reduces activity 20-fold, but increases KM only 1.9-fold; optimum pH is 5.2. Reduces binding of nickel ions. Resistant to inactivation by iodoacetamide. Ref.3 Ref.18

Mutagenesis

319

1

C → S: Reduces activity 3000-fold, but increases KM only 3.9-fold; optimum pH is 5.2. Reduces binding of nickel ions. Resistant to inactivation by iodoacetamide. Ref.3 Ref.18

Mutagenesis

319

1

C → Y: Abrogates activity. Ref.3 Ref.18

Mutagenesis

320

1

H → A: Reduces activity 100000-fold, but increases KM only 3-fold; optimum pH is 6.75. Resistant to inactivation by diethylpyrocarbonate and iodoacetamide. Ref.4 Ref.19

Mutagenesis

320

1

H → N or Q: Reduces activity 100000-fold, but increases KM only 3-fold. Ref.4 Ref.19

Mutagenesis

336

1

R → Q: Reduces activity 10000-fold, but has no effect on KM. Ref.19

Secondary structure

1

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567

Helix Strand Turn

Details...

Beta strand

3 – 5

3

Helix

6 – 13

8

Beta strand

20 – 22

3

Beta strand

29 – 31

3

Beta strand

50 – 53

4

Turn

54 – 56

3

Helix

62 – 64

3

Beta strand

67 – 77

11

Beta strand

80 – 89

10

Beta strand

92 – 97

6

Turn

102 – 104

3

Beta strand

105 – 107

3

Beta strand

109 – 111

3

Beta strand

117 – 120

4

Beta strand

125 – 128

4

Beta strand

130 – 136

7

Helix

142 – 149

8

Beta strand

151 – 157

7

Beta strand

159 – 162

4

Helix

163 – 167

5

Helix

173 – 184

12

Beta strand

187 – 196

10

Helix

202 – 211

10

Beta strand

214 – 219

6

Helix

220 – 222

3

Helix

226 – 239

14

Beta strand

242 – 246

5

Helix

256 – 263

8

Beta strand

268 – 270

3

Turn

271 – 274

4

Beta strand

278 – 280

3

Turn

281 – 283

3

Helix

284 – 289

6

Beta strand

293 – 297

5

Helix

299 – 301

3

Beta strand

305 – 307

3

Helix

308 – 320

13

Beta strand

324 – 326

3

Helix

327 – 336

10

Helix

339 – 350

12

Beta strand

356 – 358

3

Beta strand

363 – 365

3

Helix

370 – 385

16

Beta strand

393 – 395

3

Helix

397 – 404

8

Helix

405 – 407

3

Helix

409 – 414

6

Turn

418 – 420

3

Beta strand

421 – 424

4

Beta strand

432 – 435

4

Helix

437 – 439

3

Turn

440 – 442

3

Beta strand

445 – 449

5

Beta strand

452 – 458

7

Beta strand

463 – 466

4

Beta strand

472 – 475

4

Helix

477 – 479

3

Helix

481 – 487

7

Beta strand

489 – 492

4

Helix

494 – 498

5

Helix

501 – 504

4

Beta strand

509 – 513

5

Turn

517 – 519

3

Helix

522 – 524

3

Beta strand

534 – 536

3

Turn

538 – 540

3

Beta strand

543 – 545

3

Beta strand

548 – 550

3

Beta strand

555 – 557

3

Beta strand

559 – 561

3

Turn

562 – 564

3

Sequences

	Sequence		Length	Mass (Da)
	P18314 [UniParc]. Last modified November 1, 1990. Version 1. Checksum: 2ECF3C4268A2E2C7	FASTA	567	60,305
	10 20 30 40 50 60 MSNISRQAYA DMFGPTVGDK VRLADTELWI EVEDDLTTYG EEVKFGGGKV IRDGMGQGQM 70 80 90 100 110 120 LAADCVDLVL TNALIVDHWG IVKADIGVKD GRIFAIGKAG NPDIQPNVTI PIGAATEVIA 130 140 150 160 170 180 AEGKIVTAGG IDTHIHWICP QQAEEALVSG VTTMVGGGTG PAAGTHATTC TPGPWYISRM 190 200 210 220 230 240 LQAADSLPVN IGLLGKGNVS QPDALREQVA AGVIGLKIHE DWGATPAAID CALTVADEMD 250 260 270 280 290 300 IQVALHSDTL NESGFVEDTL AAIGGRTIHT FHTEGAGGGH APDIITACAH PNILPSSTNP 310 320 330 340 350 360 TLPYTLNTID EHLDMLMVCH HLDPDIAEDV AFAESRIRRE TIAAEDVLHD LGAFSLTSSD 370 380 390 400 410 420 SQAMGRVGEV ILRTWQVAHR MKVQRGALAE ETGDNDNFRV KRYIAKYTIN PALTHGIAHE 430 440 450 460 470 480 VGSIEVGKLA DLVVWSPAFF GVKPATVIKG GMIAIAPMGD INASIPTPQP VHYRPMFGAL 490 500 510 520 530 540 GSARHHCRLT FLSQAAAANG VAERLNLRSA IAVVKGCRTV QKADMVHNSL QPNITVDAQT 550 560 YEVRVDGELI TSEPADVLPM AQRYFLF

References

[1]	"Sequence of the Klebsiella aerogenes urease genes and evidence for accessory proteins facilitating nickel incorporation." Mulrooney S.B., Hausinger R.P. J. Bacteriol. 172:5837-5843(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CATALYTIC ACTIVITY. Strain: CG253.
[2]	"Klebsiella aerogenes urease gene cluster: sequence of ureD and demonstration that four accessory genes (ureD, ureE, ureF, and ureG) are involved in nickel metallocenter biosynthesis." Lee M.H., Mulrooney S.B., Renner M.J., Markowicz Y., Hausinger R.P. J. Bacteriol. 174:4324-4330(1992) [PubMed] [Europe PMC] [Abstract] Cited for: COFACTOR.
[3]	"Site-directed mutagenesis of the active site cysteine in Klebsiella aerogenes urease." Martin P.R., Hausinger R.P. J. Biol. Chem. 267:20024-20027(1992) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-319.
[4]	"Site-directed mutagenesis of Klebsiella aerogenes urease: identification of histidine residues that appear to function in nickel ligation, substrate binding, and catalysis." Park I.-S., Hausinger R.P. Protein Sci. 2:1034-1041(1993) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF HIS-134; HIS-136; HIS-219; HIS-246; HIS-320 AND HIS-320.
[5]	"In vitro activation of urease apoprotein and role of UreD as a chaperone required for nickel metallocenter assembly." Park I.-S., Carr M.B., Hausinger R.P. Proc. Natl. Acad. Sci. U.S.A. 91:3233-3237(1994) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, INTERACTION WITH UREA; UREB AND URED.
[6]	"Evidence for the presence of urease apoprotein complexes containing UreD, UreF, and UreG in cells that are competent for in vivo enzyme activation." Park I.-S., Hausinger R.P. J. Bacteriol. 177:1947-1951(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, INTERACTION WITH UREA; UREB; URED; UREF AND UREG.
[7]	"Requirement of carbon dioxide for in vitro assembly of the urease nickel metallocenter." Park I.-S., Hausinger R.P. Science 267:1156-1158(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION.
[8]	"Purification and activation properties of UreD-UreF-urease apoprotein complexes." Moncrief M.B.C., Hausinger R.P. J. Bacteriol. 178:5417-5421(1996) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, INTERACTION WITH UREA; UREB; URED AND UREF.
[9]	"GTP-dependent activation of urease apoprotein in complex with the UreD, UreF, and UreG accessory proteins." Soriano A., Hausinger R.P. Proc. Natl. Acad. Sci. U.S.A. 96:11140-11144(1999) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, INTERACTION WITH UREA; UREB; URED; UREF AND UREG.
[10]	"UreE stimulation of GTP-dependent urease activation in the UreD-UreF-UreG-urease apoprotein complex." Soriano A., Colpas G.J., Hausinger R.P. Biochemistry 39:12435-12440(2000) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, ENZYME REGULATION, ACTIVATION OF THE APOPROTEIN BY UREE.
[11]	"Dual effects of ionic strength on Klebsiella aerogenes urease: pH-dependent activation and inhibition." Mulrooney S.B., Zakharian T., Schaller R.A., Hausinger R.P. Arch. Biochem. Biophys. 394:280-282(2001) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[12]	"Chemical cross-linking and mass spectrometric identification of sites of interaction for UreD, UreF, and urease." Chang Z., Kuchar J., Hausinger R.P. J. Biol. Chem. 279:15305-15313(2004) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH UREA; UREB; URED AND UREF, MASS SPECTROMETRY.
[13]	"The crystal structure of urease from Klebsiella aerogenes." Jabri E., Carr M.B., Hausinger R.P., Karplus P.A. Science 268:998-1004(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH UREA; UREB AND NICKEL IONS, CARBAMYLATION AT LYS-217.
[14]	"Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants." Jabri E., Karplus P.A. Biochemistry 35:10616-10626(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF WILD-TYPE AND MUTANTS ALA-219 AND ALA-320 IN COMPLEX WITH UREA; UREB AND NICKEL IONS, CARBAMYLATION AT LYS-217.
[15]	"Characterization of the mononickel metallocenter in H134A mutant urease." Park I.-S., Michel L.O., Pearson M.A., Jabri E., Karplus P.A., Wang S., Dong J., Scott R.A., Koehler B.P., Johnson M.K., Hausinger R.P. J. Biol. Chem. 271:18632-18637(1996) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANT ALA-134 IN COMPLEX WITH UREA; UREB AND NICKEL IONS, MAGNETIC CIRCULAR DICHROISM, ABSORPTION SPECTROSCOPY, CARBAMYLATION AT LYS-217.
[16]	"Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease." Pearson M.A., Michel L.O., Hausinger R.P., Karplus P.A. Biochemistry 36:8164-8172(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANTS ALA/ASP/SER/TYR-319 IN COMPLEX WITH UREA; UREB; NICKEL IONS AND ACETOHYDROXAMIC ACID.
[17]	"Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand." Pearson M.A., Schaller R.A., Michel L.O., Karplus P.A., Hausinger R.P. Biochemistry 37:6214-6220(1998) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF MUTANTS ALA/CYS/GLU-217 IN COMPLEX WITH UREA; UREB AND FORMATE, MUTAGENESIS OF LYS-217.
[18]	"Characterization of metal-substituted Klebsiella aerogenes urease." Yamaguchi K., Cosper N.J., Staalhandske C., Scott R.A., Pearson M.A., Karplus P.A., Hausinger R.P. J. Biol. Inorg. Chem. 4:468-477(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) IN COMPLEX WITH UREA; UREB AND MANGANESE IONS, ABSORPTION SPECTROSCOPY, MUTAGENESIS OF CYS-319.
[19]	"Kinetic and structural characterization of urease active site variants." Pearson M.A., Park I.-S., Schaller R.A., Michel L.O., Karplus P.A., Hausinger R.P. Biochemistry 39:8575-8584(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF WILD-TYPE AND MUTANTS ASN/GLN-219; ALA-221 AND ASN/GLN-320 IN COMPLEX WITH UREA; UREB AND NICKEL IONS, CARBAMYLATION AT LYS-217, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF HIS-219; ASP-221; HIS-320 AND ARG-336.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M36068 Genomic DNA. Translation: AAA25151.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A5K	X-ray	2.20	C	2-567	[»]
1A5L	X-ray	2.20	C	2-567	[»]
1A5M	X-ray	2.00	C	2-567	[»]
1A5N	X-ray	2.40	C	2-567	[»]
1A5O	X-ray	2.50	C	2-567	[»]
1EF2	X-ray	2.50	A	2-567	[»]
1EJR	X-ray	2.00	C	1-567	[»]
1EJS	X-ray	2.00	C	1-567	[»]
1EJT	X-ray	2.00	C	1-567	[»]
1EJU	X-ray	2.00	C	1-567	[»]
1EJV	X-ray	2.40	C	1-567	[»]
1EJW	X-ray	1.90	C	1-567	[»]
1EJX	X-ray	1.60	C	1-567	[»]
1FWA	X-ray	2.00	C	1-567	[»]
1FWB	X-ray	2.00	C	1-567	[»]
1FWC	X-ray	2.00	C	1-567	[»]
1FWD	X-ray	2.00	C	1-567	[»]
1FWE	X-ray	2.00	C	1-567	[»]
1FWF	X-ray	2.00	C	1-567	[»]
1FWG	X-ray	2.00	C	1-567	[»]
1FWH	X-ray	2.00	C	1-567	[»]
1FWI	X-ray	2.00	C	1-567	[»]
1FWJ	X-ray	2.20	C	1-567	[»]
1KRA	X-ray	2.30	C	1-567	[»]
1KRB	X-ray	2.50	C	1-567	[»]
1KRC	X-ray	2.50	C	1-567	[»]
2KAU	X-ray	2.00	C	1-567	[»]
4EP8	X-ray	1.55	C	2-567	[»]
4EPB	X-ray	1.75	C	2-567	[»]
4EPD	X-ray	1.70	C	2-567	[»]
4EPE	X-ray	2.05	C	2-567	[»]

ProteinModelPortal

P18314.

SMR

P18314. Positions 2-567.

ModBase

Search...

Protein-protein interaction databases

IntAct

P18314. 3 interactions.

Protein family/group databases

MEROPS

M38.982.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

P18314.

UniPathway

UPA00258; UER00370.

Family and domain databases

HAMAP

MF_01953. Urease_alpha.

InterPro

IPR006680. Amidohydro_1.
IPR011059. Metal-dep_hydrolase_composite.
IPR011612. Urease_alpha_N.
IPR005848. Urease_asu.
IPR017951. Urease_asu_c.
IPR017950. Urease_asu_CS.
[Graphical view]

Pfam

PF01979. Amidohydro_1. 1 hit.
PF00449. Urease_alpha. 1 hit.
[Graphical view]

PRINTS

PR01752. UREASE.

SUPFAM

SSF51338. Metalo_hydrolase. 2 hits.

TIGRFAMs

TIGR01792. urease_alph. 1 hit.

PROSITE

PS01120. UREASE_1. 1 hit.
PS00145. UREASE_2. 1 hit.
PS51368. UREASE_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

DrugBank

DB00551. Acetohydroxamic Acid.

EvolutionaryTrace

P18314.

Entry information

Entry name

URE1_ENTAE

Accession

Primary (citable) accession number: P18314

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	November 1, 1990
Last modified:	May 29, 2013
This is version 118 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program