P30074 (CHS2_MEDSA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Chalcone synthase 2
EC=2.3.1.74

Alternative name(s):
Naringenin-chalcone synthase 2

Gene names

Name:

CHS2

Organism

Medicago sativa (Alfalfa)

Taxonomic identifier

3879 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › fabids › Fabales › Fabaceae › Papilionoideae › Trifolieae › Medicago

Protein attributes

Sequence length	389 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	The primary product of this enzyme is 4,2',4',6'-tetrahydroxychalcone (also termed naringenin-chalcone or chalcone) which can under specific conditions spontaneously isomerize into naringenin. Ref.3 Ref.4 Ref.5 Ref.6
Catalytic activity	3 malonyl-CoA + 4-coumaroyl-CoA = 4 CoA + naringenin chalcone + 3 CO2.
Pathway	Secondary metabolite biosynthesis; flavonoid biosynthesis.
Subunit structure	Homodimer Probable.
Sequence similarities	Belongs to the chalcone/stilbene synthases family.
Biophysicochemical properties	Kinetic parameters: KM=4.1 µM for malonyl-CoA Ref.3 Ref.4 Ref.5 KM=4.5 µM for 4-coumaroyl-CoA KM=2.2 µM for benzoyl-CoA KM=4.1 µM for hexanoyl-CoA KM=5.1 µM for phenylacetyl-CoA KM=5.2 µM for feruloyl-CoA

Ontologies

Keywords
Biological process	Flavonoid biosynthesis
Molecular function	Acyltransferase Transferase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	chalcone biosynthetic process Inferred from direct assay Ref.3. Source: UniProtKB flavonoid biosynthetic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	naringenin-chalcone synthase activity Inferred from direct assay Ref.3. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 389

389

Chalcone synthase 2

PRO_0000216007

Regions

Region

55 – 62

8

Coenzyme A binding

Region

216 – 217

2

Substrate binding

Sites

Active site

164

1

Acyl-thioester intermediate Probable

Binding site

197

1

Substrate

Binding site

308

1

Coenzyme A; via amide nitrogen

Experimental info

Mutagenesis

164

1

C → A, D or S: Loss of activity. Ref.3

Mutagenesis

215

1

F → S, W or Y: Drastically reduces catalytic efficiency. Ref.3 Ref.5

Mutagenesis

256

1

G → A: Decreases catalytic efficiency 2-fold. Ref.4

Mutagenesis

256

1

G → F or L: Drastically reduces catalytic efficiency. Ref.4

Mutagenesis

256

1

G → V: Decreases catalytic efficiency 7-fold. Ref.4

Mutagenesis

265

1

F → V: Decreases catalytic efficiency 2-fold. Ref.5

Mutagenesis

303

1

H → A, D, N or T: Drastically reduces catalytic efficiency. Ref.3

Mutagenesis

303

1

H → Q: Decreases catalytic efficiency 13-fold. Ref.3

Mutagenesis

336

1

N → A, D, H, K or Q: Drastically reduces catalytic efficiency. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

389

Helix Strand Turn

Details...

Helix

4 – 11

8

Beta strand

18 – 25

8

Beta strand

30 – 32

3

Helix

33 – 35

3

Helix

36 – 43

8

Helix

50 – 62

13

Beta strand

67 – 69

3

Helix

74 – 79

6

Helix

81 – 84

4

Beta strand

85 – 87

3

Helix

91 – 117

27

Helix

121 – 123

3

Beta strand

126 – 133

8

Beta strand

136 – 138

3

Helix

140 – 148

9

Beta strand

155 – 161

7

Helix

166 – 179

14

Beta strand

185 – 192

8

Helix

194 – 196

3

Helix

206 – 214

9

Beta strand

218 – 227

10

Turn

230 – 232

3

Beta strand

237 – 246

10

Beta strand

253 – 259

7

Beta strand

262 – 267

6

Helix

271 – 287

17

Helix

288 – 290

3

Beta strand

297 – 302

6

Helix

307 – 317

11

Helix

321 – 324

4

Helix

325 – 334

10

Helix

338 – 340

3

Helix

341 – 355

15

Turn

361 – 364

4

Beta strand

366 – 374

9

Turn

375 – 377

3

Beta strand

378 – 386

9

Sequences

	Sequence		Length	Mass (Da)
	P30074 [UniParc]. Last modified April 1, 1993. Version 1. Checksum: E03422EE332A5408	FASTA	389	42,706
	10 20 30 40 50 60 MVSVSEIRKA QRAEGPATIL AIGTANPANC VEQSTYPDFY FKITNSEHKT ELKEKFQRMC 70 80 90 100 110 120 DKSMIKRRYM YLTEEILKEN PNVCEYMAPS LDARQDMVVV EVPRLGKEAA VKAIKEWGQP 130 140 150 160 170 180 KSKITHLIVC TTSGVDMPGA DYQLTKLLGL RPYVKRYMMY QQGCFAGGTV LRLAKDLAEN 190 200 210 220 230 240 NKGARVLVVC SEVTAVTFRG PSDTHLDSLV GQALFGDGAA ALIVGSDPVP EIEKPIFEMV 250 260 270 280 290 300 WTAQTIAPDS EGAIDGHLRE AGLTFHLLKD VPGIVSKNIT KALVEAFEPL GISDYNSIFW 310 320 330 340 350 360 IAHPGGPAIL DQVEQKLALK PEKMNATREV LSEYGNMSSA CVLFILDEMR KKSTQNGLKT 370 380 TGEGLEWGVL FGFGPGLTIE TVVLRSVAI

References

[1]	"Stress responses in alfalfa (Medicago sativa L.). 15. Characterization and expression patterns of members of a subset of the chalcone synthase multigene family." Junghans H., Dalkin K., Dixon R.A. Plant Mol. Biol. 22:239-253(1993) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis." Ferrer J.L., Jez J.M., Bowman M.E., Dixon R.A., Noel J.P. Nat. Struct. Biol. 6:775-784(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.56 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND COENZYME A.
[3]	"Dissection of malonyl-coenzyme A decarboxylation from polyketide formation in the reaction mechanism of a plant polyketide synthase." Jez J.M., Ferrer J.L., Bowman M.E., Dixon R.A., Noel J.P. Biochemistry 39:890-902(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.69 ANGSTROMS) IN COMPLEX WITH COENZYME A, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF CYS-164; PHE-215; HIS-303 AND ASN-336.
[4]	"Structure-guided programming of polyketide chain-length determination in chalcone synthase." Jez J.M., Bowman M.E., Noel J.P. Biochemistry 40:14829-14838(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF GLY-256.
[5]	"Expanding the biosynthetic repertoire of plant type III polyketide synthases by altering starter molecule specificity." Jez J.M., Bowman M.E., Noel J.P. Proc. Natl. Acad. Sci. U.S.A. 99:5319-5324(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS), FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF PHE-215 AND PHE-265.
[6]	"An aldol switch discovered in stilbene synthases mediates cyclization specificity of type III polyketide synthases." Austin M.B., Bowman M.E., Ferrer J.-L., Schroeder J., Noel J.P. Chem. Biol. 11:1179-1194(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS), FUNCTION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L02902 mRNA. Translation: AAA02824.1.

PIR

S35164.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1BI5	X-ray	1.56	A	1-389	[»]
1BQ6	X-ray	1.56	A	2-389	[»]
1CGK	X-ray	1.84	A	1-389	[»]
1CGZ	X-ray	1.70	A	1-389	[»]
1CHW	X-ray	1.90	A/B	1-389	[»]
1CML	X-ray	1.69	A	1-389	[»]
1D6F	X-ray	1.69	A	1-389	[»]
1D6H	X-ray	2.15	A	3-389	[»]
1D6I	X-ray	2.00	A/B	2-389	[»]
1I86	X-ray	1.50	A	1-389	[»]
1I88	X-ray	1.45	A/B	1-389	[»]
1I89	X-ray	1.86	A/B	1-389	[»]
1I8B	X-ray	1.95	A/B	1-389	[»]
1JWX	X-ray	1.63	A	1-389	[»]
1U0V	X-ray	1.90	A/B	1-389	[»]
1U0W	X-ray	2.00	A/B/C/D	1-389	[»]

ProteinModelPortal

P30074.

SMR

P30074. Positions 3-389.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

UniPathway

UPA00154.

Family and domain databases

Gene3D

3.40.47.10. 2 hits.

InterPro

IPR012328. Chalcone/stilbene_synth_C.
IPR018088. Chalcone/stilbene_synthase_AS.
IPR001099. Chalcone/stilbene_synthase_N.
IPR011141. Polyketide_synthase_type-III.
IPR016039. Thiolase-like.
IPR016038. Thiolase-like_subgr.
[Graphical view]

Pfam

PF02797. Chal_sti_synt_C. 1 hit.
PF00195. Chal_sti_synt_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000451. PKS_III. 1 hit.

SUPFAM

SSF53901. Thiolase-like. 2 hits.

PROSITE

PS00441. CHALCONE_SYNTH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P30074.

Entry information

Entry name

CHS2_MEDSA

Accession

Primary (citable) accession number: P30074

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1993
Last sequence update:	April 1, 1993
Last modified:	April 3, 2013
This is version 80 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program