P09546 (PUTA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional protein putA

Including the following 2 domains:

1. Proline dehydrogenase
   EC=1.5.99.8
   Alternative name(s):
   Proline oxidase
2. Delta-1-pyrroline-5-carboxylate dehydrogenase
   Short name=P5C dehydrogenase
   EC=1.5.1.12

Gene names

Name:	putA
Synonyms:	poaA
Ordered Locus Names:	b1014, JW0999

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	1320 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon.
Catalytic activity	L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor. (S)-1-pyrroline-5-carboxylate + NAD(P)+ + 2 H2O = L-glutamate + NAD(P)H.
Cofactor	FAD.
Pathway	Amino-acid degradation; L-proline degradation into L-glutamate; L-glutamate from L-proline: step 1/2. Amino-acid degradation; L-proline degradation into L-glutamate; L-glutamate from L-proline: step 2/2.
Subunit structure	Homodimer. Ref.6
Induction	By proline, autorepression and catabolite repression, and is potentially nitrogen controlled.
Sequence similarities	In the N-terminal section; belongs to the proline dehydrogenase family. In the C-terminal section; belongs to the aldehyde dehydrogenase family.

Ontologies

Keywords
Biological process	Proline metabolism Transcription Transcription regulation
Ligand	DNA-binding FAD Flavoprotein NAD
Molecular function	Oxidoreductase Repressor
Technical term	3D-structure Complete proteome Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological process	glutamate biosynthetic process Inferred from electronic annotation. Source: InterPro proline biosynthetic process Inferred from electronic annotation. Source: InterPro proline catabolic process to glutamate Inferred from mutant phenotype. Source: EcoCyc transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	1-pyrroline-5-carboxylate dehydrogenase activity Inferred from direct assay. Source: EcoCyc DNA binding Inferred from direct assay. Source: EcoCyc flavin adenine dinucleotide binding Inferred from direct assay. Source: EcoCyc oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor Inferred from electronic annotation. Source: InterPro proline dehydrogenase activity Inferred from direct assay. Source: EcoCyc sequence-specific DNA binding transcription factor activity Inferred from direct assay. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1320

1320

Bifunctional protein putA

PRO_0000056524

Regions

Region

228 – 574

347

Proline dehydrogenase

Region

653 – 1119

467

Aldehyde dehydrogenase

Sites

Active site

883

1

By similarity

Active site

917

1

By similarity

Experimental info

Sequence conflict

531

1

G → A in AAB59985. Ref.1

Secondary structure

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1320

Helix Strand Turn

Details...

Beta strand

4 – 10

7

Helix

12 – 24

13

Helix

29 – 43

15

Helix

90 – 97

8

Turn

98 – 100

3

Helix

103 – 114

12

Helix

118 – 136

19

Turn

137 – 140

4

Helix

141 – 153

13

Turn

154 – 156

3

Helix

161 – 173

13

Helix

178 – 187

10

Turn

188 – 192

5

Turn

203 – 206

4

Helix

210 – 214

5

Helix

225 – 235

11

Turn

236 – 239

4

Helix

241 – 256

16

Helix

257 – 259

3

Beta strand

261 – 264

4

Helix

265 – 276

12

Turn

277 – 279

3

Beta strand

281 – 286

6

Helix

294 – 315

22

Helix

319 – 322

4

Beta strand

325 – 328

4

Helix

330 – 332

3

Helix

337 – 339

3

Helix

342 – 363

22

Beta strand

367 – 369

3

Helix

374 – 376

3

Helix

377 – 387

11

Helix

391 – 393

3

Beta strand

399 – 404

6

Helix

410 – 423

14

Beta strand

428 – 433

6

Helix

438 – 448

11

Helix

459 – 474

16

Turn

477 – 479

3

Beta strand

480 – 485

6

Helix

489 – 498

10

Helix

505 – 507

3

Beta strand

509 – 513

5

Turn

514 – 516

3

Helix

518 – 521

4

Turn

522 – 524

3

Helix

528 – 530

3

Beta strand

537 – 543

7

Helix

546 – 548

3

Helix

550 – 561

12

Helix

566 – 569

4

Helix

577 – 580

4

Helix

584 – 595

12

Beta strand

596 – 599

4

Sequences

	Sequence		Length	Mass (Da)
	P09546 [UniParc]. Last modified November 1, 1997. Version 3. Checksum: E4920143D536F7F9	FASTA	1,320	143,815
	10 20 30 40 50 60 MGTTTMGVKL DDATRERIKS AATRIDRTPH WLIKQAIFSY LEQLENSDTL PELPALLSGA 70 80 90 100 110 120 ANESDEAPTP AEEPHQPFLD FAEQILPQSV SRAAITAAYR RPETEAVSML LEQARLPQPV 130 140 150 160 170 180 AEQAHKLAYQ LADKLRNQKN ASGRAGMVQG LLQEFSLSSQ EGVALMCLAE ALLRIPDKAT 190 200 210 220 230 240 RDALIRDKIS NGNWQSHIGR SPSLFVNAAT WGLLFTGKLV STHNEASLSR SLNRIIGKSG 250 260 270 280 290 300 EPLIRKGVDM AMRLMGEQFV TGETIAEALA NARKLEEKGF RYSYDMLGEA ALTAADAQAY 310 320 330 340 350 360 MVSYQQAIHA IGKASNGRGI YEGPGISIKL SALHPRYSRA QYDRVMEELY PRLKSLTLLA 370 380 390 400 410 420 RQYDIGINID AEESDRLEIS LDLLEKLCFE PELAGWNGIG FVIQAYQKRC PLVIDYLIDL 430 440 450 460 470 480 ATRSRRRLMI RLVKGAYWDS EIKRAQMDGL EGYPVYTRKV YTDVSYLACA KKLLAVPNLI 490 500 510 520 530 540 YPQFATHNAH TLAAIYQLAG QNYYPGQYEF QCLHGMGEPL YEQVTGKVAD GKLNRPCRIY 550 560 570 580 590 600 APVGTHETLL AYLVRRLLEN GANTSFVNRI ADTSLPLDEL VADPVTAVEK LAQQEGQTGL 610 620 630 640 650 660 PHPKIPLPRD LYGHGRDNSA GLDLANEHRL ASLSSALLNS ALQKWQALPM LEQPVAAGEM 670 680 690 700 710 720 SPVINPAEPK DIVGYVREAT PREVEQALES AVNNAPIWFA TPPAERAAIL HRAAVLMESQ 730 740 750 760 770 780 MQQLIGILVR EAGKTFSNAI AEVREAVDFL HYYAGQVRDD FANETHRPLG PVVCISPWNF 790 800 810 820 830 840 PLAIFTGQIA AALAAGNSVL AKPAEQTPLI AAQGIAILLE AGVPPGVVQL LPGRGETVGA 850 860 870 880 890 900 QLTGDDRVRG VMFTGSTEVA TLLQRNIASR LDAQGRPIPL IAETGGMNAM IVDSSALTEQ 910 920 930 940 950 960 VVVDVLASAF DSAGQRCSAL RVLCLQDEIA DHTLKMLRGA MAECRMGNPG RLTTDIGPVI 970 980 990 1000 1010 1020 DSEAKANIER HIQTMRSKGR PVFQAVRENS EDAREWQSGT FVAPTLIELD DFAELQKEVF 1030 1040 1050 1060 1070 1080 GPVLHVVRYN RNQLPELIEQ INASGYGLTL GVHTRIDETI AQVTGSAHVG NLYVNRNMVG 1090 1100 1110 1120 1130 1140 AVVGVQPFGG EGLSGTGPKA GGPLYLYRLL ANRPESALAV TLARQDAKYP VDAQLKAALT 1150 1160 1170 1180 1190 1200 QPLNALREWA ANRPELQALC TQYGELAQAG TQRLLPGPTG ERNTWTLLPR ERVLCIADDE 1210 1220 1230 1240 1250 1260 QDALTQLAAV LAVGSQVLWP DDALHRQLVK ALPSAVSERI QLAKAENITA QPFDAVIFHG 1270 1280 1290 1300 1310 1320 DSDQLRALCE AVAARDGTIV SVQGFARGES NILLERLYIE RSLSVNTAAA GGNASLMTIG

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence analysis identifies the proline dehydrogenase and delta 1-pyrroline-5-carboxylate dehydrogenase domains of the multifunctional Escherichia coli PutA protein." Ling M., Allen S.W., Wood J.M. J. Mol. Biol. 243:950-956(1994) [PubMed: 7966312] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. , Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. DNA Res. 3:137-155(1996) [PubMed: 8905232] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Nucleotide sequence of putC, the regulatory region for the put regulon of Escherichia coli K12." Nakao T., Yamato I., Anraku Y. Mol. Gen. Genet. 210:364-368(1987) [PubMed: 3325781] [Abstract] Cited for: PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-60. Strain: K12.
[6]	"Structure of the proline dehydrogenase domain of the multifunctional PutA flavoprotein." Lee Y.-H., Nadaraia S., Gu D., Becker D.F., Tanner J.J. Nat. Struct. Biol. 10:109-114(2003) [PubMed: 12514740] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-669 IN COMPLEX WITH FAD, HOMODIMERIZATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U05212 Genomic DNA. Translation: AAB59985.1.
U00096 Genomic DNA. Translation: AAC74099.1.
AP009048 Genomic DNA. Translation: BAA35791.1.
X05653 Genomic DNA. Translation: CAA29141.1. Sequence problems.

PIR

D64843.

RefSeq

NP_415534.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1K87	X-ray	2.00	A	1-669	[»]
1TIW	X-ray	2.00	A	86-669	[»]
1TJ0	X-ray	2.10	A	86-669	[»]
1TJ1	X-ray	2.00	A	86-669	[»]
1TJ2	X-ray	2.05	A	86-669	[»]
2AY0	X-ray	2.10	A/B/C/D/E/F	1-52	[»]
2FZM	X-ray	2.30	A	86-669	[»]
2FZN	X-ray	2.00	A	86-669	[»]
2GPE	X-ray	1.90	A/B/C/D	1-52	[»]
2RBF	X-ray	2.25	A/B	1-52	[»]
3E2Q	X-ray	1.75	A	86-630	[»]
3E2R	X-ray	1.85	A	86-630	[»]
3E2S	X-ray	2.00	A	86-630	[»]
3ITG	X-ray	2.15	A/B	86-669	[»]

ProteinModelPortal

P09546.

SMR

P09546. Positions 2-49, 87-612, 614-1114.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10620N.

IntAct

P09546. 21 interactions.

MINT

MINT-1267731.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000000125; EBESCP00000000125; EBESCG00000000099.
EBESCT00000016874; EBESCP00000016165; EBESCG00000015933.

GeneID

945600.

GenomeReviews

Gene locus JW0999 in contig AP009048_GR.
Gene locus b1014 in contig U00096_GR.

KEGG

ecj:JW0999.
eco:b1014.

PATRIC

32117257. VBIEscCol129921_1052.

Organism-specific databases

EchoBASE

EB0794.

EcoGene

EG10801. putA.

Phylogenomic databases

eggNOG

COG4230.

GeneTree

EBGT00050000009176.

HOGENOM

HBG288861.

OMA

QPFLEFA.

PhylomeDB

P09546.

ProtClustDB

PRK11809.

Enzyme and pathway databases

BioCyc

EcoCyc:PUTA-MONOMER.
MetaCyc:PUTA-MONOMER.

Gene expression databases

Genevestigator

P09546.

Family and domain databases

InterPro

IPR016161. Ald_DH/histidinol_DH.
IPR016163. Ald_DH_C.
IPR016160. Ald_DH_CS.
IPR016162. Ald_DH_N.
IPR015590. Aldehyde_DH_dom.
IPR005933. Delta1-pyrroline-5-COlate_DH-3.
IPR024090. PRODH_PutA_dom_I.
IPR024089. PRODH_PutA_dom_I/II.
IPR024082. PRODH_PutA_dom_II.
IPR002872. Proline_DH.
[Graphical view]

Gene3D

G3DSA:3.40.309.10. Aldehyde_dehydrogenase_C. 1 hit.
G3DSA:3.40.605.10. Aldehyde_dehydrogenase_N. 1 hit.
G3DSA:1.10.2060.10. G3DSA:1.10.2060.10. 1 hit.
G3DSA:1.20.5.550. G3DSA:1.20.5.550. 1 hit.

KO

K13821.

Pfam

PF00171. Aldedh. 1 hit.
PF01619. Pro_dh. 1 hit.
[Graphical view]

SUPFAM

SSF53720. Aldehyde_DH/Histidinol_DH. 1 hit.
SSF81935. SSF81935. 1 hit.

TIGRFAMs

TIGR01238. D1pyr5carbox3. 1 hit.

PROSITE

PS00070. ALDEHYDE_DEHYDR_CYS. 1 hit.
PS00687. ALDEHYDE_DEHYDR_GLU. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

PUTA_ECOLI

Accession

Primary (citable) accession number: P09546
Secondary accession number(s): P78296

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 1, 1989
Last sequence update:	November 1, 1997
Last modified:	January 25, 2012
This is version 132 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program