O31156 (PHNX_BACCE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Phosphonoacetaldehyde hydrolase
Short name=Phosphonatase
EC=3.11.1.1

Alternative name(s):
Phosphonoacetaldehyde phosphonohydrolase

Gene names

Name:

phnX

Organism

Bacillus cereus

Taxonomic identifier

1396 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus cereus group

Protein attributes

Sequence length	264 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in phosphonate degradation. HAMAP-Rule MF_01375
Catalytic activity	Phosphonoacetaldehyde + H2O = acetaldehyde + phosphate. HAMAP-Rule MF_01375
Cofactor	Binds 1 Mg2+ ion per subunit.
Subunit structure	Homodimer. Ref.3
Sequence similarities	Belongs to the HAD-like hydrolase superfamily. PhnX family.
Biophysicochemical properties	Kinetic parameters: KM=33 µM for phosphonoacetaldehyde (at pH 7.0, 25 degrees Celsius) HAMAP-Rule MF_01375
Sequence caution	The sequence AAB86434.2 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Ligand	Magnesium Metal-binding Schiff base
Molecular function	Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	organic phosphonate catabolic process Inferred from electronic annotation. Source: InterPro
Molecular_function	magnesium ion binding Inferred from electronic annotation. Source: HAMAP phosphoglycolate phosphatase activity Inferred from electronic annotation. Source: InterPro phosphonoacetaldehyde hydrolase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 264

264

Phosphonoacetaldehyde hydrolase HAMAP-Rule MF_01375

PRO_0000284575

Sites

Active site

9

1

Nucleophile

Active site

50

1

Schiff-base intermediate with substrate

Metal binding

9

1

Magnesium

Metal binding

11

1

Magnesium; via carbonyl oxygen

Metal binding

183

1

Magnesium

Experimental info

Mutagenesis

9

1

D → A: Loss of enzymatic activity. Ref.4 Ref.7

Mutagenesis

9

1

D → E: Kcat/KM decreases 30000-fold. Ref.4 Ref.7

Mutagenesis

19

1

C → A or S: Kcat/KM decreases 10-100-fold. Ref.5

Mutagenesis

46

1

M → L: Kcat/KM decreases 17000-fold. Ref.5

Mutagenesis

47

1

G → A: Kcat/KM decreases 10000-fold. Ref.6

Mutagenesis

47

1

G → P or V: Loss of enzymatic activity. Ref.6

Mutagenesis

50

1

K → R: Loss of enzymatic activity. Ref.6

Mutagenesis

53

1

H → A: Kcat/KM decreases 1000-fold. Ref.5 Ref.8

Mutagenesis

53

1

H → Q: Kcat/KM decreases 250-fold. Ref.5 Ref.8

Mutagenesis

125

1

Y → A: Kcat/KM decreases 230-fold. Ref.5

Mutagenesis

125

1

Y → F: Kcat/KM decreases 10-fold. Ref.5

Mutagenesis

183

1

D → A: Loss of enzymatic activity. Ref.7

Mutagenesis

187

1

D → A: Kcat/KM decreases 10000-fold. Ref.7

Secondary structure

1

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264

Helix Strand Turn

Details...

Beta strand

5 – 8

4

Turn

11 – 13

3

Beta strand

14 – 16

3

Helix

23 – 31

9

Turn

32 – 34

3

Helix

39 – 43

5

Turn

44 – 47

4

Helix

50 – 59

10

Helix

61 – 71

11

Helix

77 – 94

18

Helix

95 – 98

4

Helix

105 – 114

10

Beta strand

118 – 122

5

Helix

127 – 139

13

Helix

150 – 152

3

Beta strand

153 – 155

3

Beta strand

157 – 160

4

Helix

161 – 170

10

Helix

175 – 177

3

Beta strand

178 – 184

7

Helix

185 – 193

9

Beta strand

196 – 201

6

Turn

206 – 208

3

Helix

212 – 217

6

Helix

220 – 236

17

Beta strand

240 – 245

6

Helix

246 – 248

3

Helix

249 – 256

8

Sequences

	Sequence		Length	Mass (Da)
	O31156 [UniParc]. Last modified April 17, 2007. Version 3. Checksum: 59A99D2BBED760AD	FASTA	264	30,060
	10 20 30 40 50 60 MKIEAVIFDW AGTTVDYGCF APLEVFMEIF HKRGVAITAE EARKPMGLLK IDHVRALTEM 70 80 90 100 110 120 PRIASEWNRV FRQLPTEADI QEMYEEFEEI LFAILPRYAS PINGVKEVIA SLRERGIKIG 130 140 150 160 170 180 STTGYTREMM DIVAKEAALQ GYKPDFLVTP DDVPAGRPYP WMCYKNAMEL GVYPMNHMIK 190 200 210 220 230 240 VGDTVSDMKE GRNAGMWTVG VILGSSELGL TEEEVENMDS VELREKIEVV RNRFVENGAH 250 260 FTIETMQELE SVMEHIEKQE LIIS

References

[1]	"Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis." Baker A.S., Ciocci M.J., Metcalf W.W., Kim J., Babbitt P.C., Wanner B.L., Martin B.M., Dunaway-Mariano D. Biochemistry 37:9305-9315(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-17 AND 35-55, REACTION MECHANISM, BIOPHYSICAL CHARACTERIZATION. Strain: ATCC 43881 / AI-2.
[2]	"Investigation of the substrate binding and catalytic groups of the P-C bond cleaving enzyme, phosphonoacetaldehyde hydrolase." Olsen D.B., Hepburn T.W., Lee S.-L., Martin B.M., Mariano P.S., Dunaway-Mariano D. Arch. Biochem. Biophys. 296:144-151(1992) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 34-55, SCHIFF BASE, REACTION MECHANISM. Strain: ATCC 43881 / AI-2.
[3]	"Crystallization and preliminary crystallographic analysis of phosphonoacetaldehyde hydrolase." Morais M.C., Baker A.S., Dunaway-Mariano D., Allen K.N. Acta Crystallogr. D 56:206-209(2000) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT, PRELIMINARY CRYSTALLOGRAPHY. Strain: ATCC 43881 / AI-2.
[4]	"The crystal structure of Bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily." Morais M.C., Zhang W., Baker A.S., Zhang G., Dunaway-Mariano D., Allen K.N. Biochemistry 39:10385-10396(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 2-260 IN COMPLEX WITH THE PHOSPHATE ANALOG TUNGSTATE, BINDING OF MAGNESIUM, MUTAGENESIS OF ASP-9. Strain: ATCC 43881 / AI-2.
[5]	"X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis." Morais M.C., Zhang G., Zhang W., Olsen D.B., Dunaway-Mariano D., Allen K.N. J. Biol. Chem. 279:9353-9361(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) IN COMPLEX WITH MG(2+) AND WITH MG(2+) PLUS VINYLSULFONATE, MUTAGENESIS OF CYS-19; MET-46; HIS-53 AND TYR-125. Strain: ATCC 43881 / AI-2.
[6]	"Analysis of the substrate specificity loop of the HAD superfamily cap domain." Lahiri S.D., Zhang G., Dai J., Dunaway-Mariano D., Allen K.N. Biochemistry 43:2812-2820(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF MUTANT PRO-47, MUTAGENESIS OF GLY-47 AND LYS-50. Strain: ATCC 43881 / AI-2.
[7]	"Investigation of metal ion binding in phosphonoacetaldehyde hydrolase identifies sequence markers for metal-activated enzymes of the HAD enzyme superfamily." Zhang G., Morais M.C., Dai J., Zhang W., Dunaway-Mariano D., Allen K.N. Biochemistry 43:4990-4997(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT ALA-9 IN COMPLEX WITH MG(2+) AND WITH MG(2+) PLUS PHOSPHONOACETALDEHYDE, MUTAGENESIS OF ASP-9; ASP-183 AND ASP-187. Strain: ATCC 43881 / AI-2.
[8]	"Diversification of function in the haloacid dehalogenase enzyme superfamily: the role of the cap domain in hydrolytic phosphorus--carbon bond cleavage." Lahiri S.D., Zhang G., Dunaway-Mariano D., Allen K.N. Bioorg. Chem. 34:394-409(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF MUTANT ARG-50, MUTAGENESIS OF HIS-53. Strain: ATCC 43881 / AI-2.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF030979 Genomic DNA. Translation: AAB86434.2. Different initiation.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FEZ	X-ray	3.00	A/B/C/D	2-257	[»]
1RDF	X-ray	2.80	A/B/C/D/E/F	1-264	[»]
1RQL	X-ray	2.40	A/B	1-264	[»]
1RQN	X-ray	2.80	A/B	1-264	[»]
1SWV	X-ray	2.30	A/B	1-264	[»]
1SWW	X-ray	2.30	A/B	1-264	[»]
2IOF	X-ray	2.50	A/K	1-264	[»]
2IOH	X-ray	2.90	A/B/C/D	1-264	[»]

ProteinModelPortal

O31156.

SMR

O31156. Positions 2-257.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

SABIO-RK

O31156.

Family and domain databases

Gene3D

1.10.150.240. 1 hit.
3.40.50.1000. 2 hits.

HAMAP

MF_01375. PhnX.

InterPro

IPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA_v1.
IPR006402. HAD-SF_hydro_IA_v3.
IPR023198. PGP_dom2.
IPR006323. Phosphonoacetald_hydro.
[Graphical view]

Pfam

PF13419. HAD_2. 1 hit.
[Graphical view]

SUPFAM

SSF56784. HAD-like_dom. 1 hit.

TIGRFAMs

TIGR01549. HAD-SF-IA-v1. 1 hit.
TIGR01509. HAD-SF-IA-v3. 1 hit.
TIGR01422. phosphonatase. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

O31156.

Entry information

Entry name

PHNX_BACCE

Accession

Primary (citable) accession number: O31156

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 17, 2007
Last sequence update:	April 17, 2007
Last modified:	April 3, 2013
This is version 64 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program