P25526 (GABD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Succinate-semialdehyde dehydrogenase [NADP+] GabD
Short name=SSDH
EC=1.2.1.79

Gene names

Name:	gabD
Ordered Locus Names:	b2661, JW2636

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	482 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the NADP+-dependent oxidation of succinate semialdehyde to succinate. It appears to be important for nitrogen metabolism under N limitation conditions. Ref.5 Ref.7
Catalytic activity	Succinate semialdehyde + NADP+ + H2O = succinate + NADPH. Ref.7
Pathway	Amino-acid degradation; 4-aminobutanoate degradation.
Subunit structure	Homotetramer. Ref.7
Induction	Induced by RpoS in response to multiple stress conditions, including shifts to acidic pH, nitrogen limitation or high osmolarity as well as starvation or stationary phase. Induced by gamma-aminobutyrate (GABA). Ref.5 Ref.6
Sequence similarities	Belongs to the aldehyde dehydrogenase family.
Biophysicochemical properties	Kinetic parameters: The enzyme activity measured in the presence of NADP+ is approximately 20-fold higher than that measured in the presence of NAD+. KM=16.94 µM for succinate semialdehyde Ref.7

Ontologies

Keywords
Ligand	NADP
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	gamma-aminobutyric acid catabolic process Inferred from direct assay Ref.5. Source: UniProtKB
Cellular component	cytoplasm Inferred from direct assay. Source: EcoliWiki
Molecular function	succinate-semialdehyde dehydrogenase [NAD(P)+] activity Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 482

482

Succinate-semialdehyde dehydrogenase [NADP+] GabD

PRO_0000056572

Regions

Nucleotide binding

156 – 157

2

NADP

Nucleotide binding

180 – 183

4

NADP

Nucleotide binding

233 – 234

2

NADP

Sites

Active site

255

1

Proton acceptor

Active site

289

1

Nucleophile

Binding site

256

1

NADP; via carbonyl oxygen

Binding site

386

1

NADP

Secondary structure

1

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482

Helix Strand Turn

Details...

Helix

6 – 8

3

Beta strand

12 – 14

3

Beta strand

42 – 44

3

Helix

48 – 66

19

Helix

69 – 85

17

Helix

87 – 97

11

Helix

102 – 105

4

Helix

109 – 121

13

Beta strand

139 – 146

8

Beta strand

150 – 153

4

Beta strand

156 – 158

3

Helix

161 – 164

4

Turn

170 – 172

3

Beta strand

177 – 180

4

Helix

187 – 198

12

Beta strand

206 – 208

3

Helix

219 – 222

4

Beta strand

228 – 231

4

Helix

240 – 245

6

Turn

246 – 249

4

Beta strand

251 – 254

4

Beta strand

260 – 264

5

Helix

270 – 274

5

Helix

278 – 282

5

Beta strand

291 – 298

8

Helix

302 – 313

12

Helix

334 – 349

16

Beta strand

353 – 356

4

Beta strand

368 – 375

8

Helix

381 – 383

3

Beta strand

391 – 397

7

Helix

400 – 408

9

Beta strand

417 – 419

3

Helix

423 – 428

6

Beta strand

448 – 450

3

Helix

470 – 472

3

Beta strand

473 – 480

8

Sequences

	Sequence		Length	Mass (Da)
	P25526 [UniParc]. Last modified May 1, 1992. Version 1. Checksum: 091538F8741DB0CF	FASTA	482	51,720
	10 20 30 40 50 60 MKLNDSNLFR QQALINGEWL DANNGEAIDV TNPANGDKLG SVPKMGADET RAAIDAANRA 70 80 90 100 110 120 LPAWRALTAK ERATILRNWF NLMMEHQDDL ARLMTLEQGK PLAEAKGEIS YAASFIEWFA 130 140 150 160 170 180 EEGKRIYGDT IPGHQADKRL IVIKQPIGVT AAITPWNFPA AMITRKAGPA LAAGCTMVLK 190 200 210 220 230 240 PASQTPFSAL ALAELAIRAG VPAGVFNVVT GSAGAVGNEL TSNPLVRKLS FTGSTEIGRQ 250 260 270 280 290 300 LMEQCAKDIK KVSLELGGNA PFIVFDDADL DKAVEGALAS KFRNAGQTCV CANRLYVQDG 310 320 330 340 350 360 VYDRFAEKLQ QAVSKLHIGD GLDNGVTIGP LIDEKAVAKV EEHIADALEK GARVVCGGKA 370 380 390 400 410 420 HERGGNFFQP TILVDVPANA KVSKEETFGP LAPLFRFKDE ADVIAQANDT EFGLAAYFYA 430 440 450 460 470 480 RDLSRVFRVG EALEYGIVGI NTGIISNEVA PFGGIKASGL GREGSKYGIE DYLEIKYMCI GL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular organization of the Escherichia coli gab cluster: nucleotide sequence of the structural genes gabD and gabP and expression of the GABA permease gene." Niegemann E., Schulz A., Bartsch K. Arch. Microbiol. 160:454-460(1993) [PubMed: 8297211] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / JM103 / ATCC 39403 / DSM 2829 / NCIMB 12044.
[2]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [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], SEQUENCE REVISION. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Succinic semialdehyde dehydrogenases of Escherichia coli: their role in the degradation of p-hydroxyphenylacetate and gamma-aminobutyrate." Donnelly M.I., Cooper R.A. Eur. J. Biochem. 113:555-561(1981) [PubMed: 7011797] [Abstract] Cited for: FUNCTION AS NADP-DEPENDENT SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, NADP, INDUCTION. Strain: K12.
[6]	"Multiple stress signal integration in the regulation of the complex sigma S-dependent csiD-ygaF-gabDTP operon in Escherichia coli." Metzner M., Germer J., Hengge R. Mol. Microbiol. 51:799-811(2004) [PubMed: 14731280] [Abstract] Cited for: INDUCTION. Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[7]	"The X-ray crystal structure of Escherichia coli succinic semialdehyde dehydrogenase; structural insights into NADP+/enzyme interactions." Langendorf C.G., Key T.L., Fenalti G., Kan W.T., Buckle A.M., Caradoc-Davies T., Tuck K.L., Law R.H., Whisstock J.C. PLoS ONE 5:E9280-E9280(2010) [PubMed: 20174634] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NADP(+), FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, REACTION MECHANISM, SUBUNIT. Strain: K12.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M88334 Genomic DNA. Translation: AAC36831.1.
U00096 Genomic DNA. Translation: AAC75708.1.
AP009048 Genomic DNA. Translation: BAA16524.2.

PIR

F65045.

RefSeq

NP_417147.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3JZ4	X-ray	2.30	A/B/C/D	2-482	[»]

ProteinModelPortal

P25526.

SMR

P25526. Positions 2-482.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9723N.

IntAct

P25526. 2 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001833; EBESCP00000001833; EBESCG00000001513.
EBESCT00000001834; EBESCP00000001834; EBESCG00000001513.
EBESCT00000001835; EBESCP00000001835; EBESCG00000001513.
EBESCT00000017273; EBESCP00000016564; EBESCG00000016332.

GeneID

948060.

GenomeReviews

Gene locus JW2636 in contig AP009048_GR.
Gene locus b2661 in contig U00096_GR.

KEGG

ecj:JW2636.
eco:b2661.

PATRIC

32120712. VBIEscCol129921_2753.

Organism-specific databases

EchoBASE

EB1305.

EcoGene

EG11329. gabD.

Phylogenomic databases

eggNOG

COG1012.

GeneTree

EBGT00050000009175.

HOGENOM

HBG752218.

OMA

QTIKVTN.

PhylomeDB

P25526.

ProtClustDB

PRK11241.

Enzyme and pathway databases

BioCyc

EcoCyc:SUCCSEMIALDDEHYDROG-MONOMER.
MetaCyc:SUCCSEMIALDDEHYDROG-MONOMER.

Gene expression databases

Genevestigator

P25526.

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.
IPR010102. Succ_semiAld_DH.
[Graphical view]

Gene3D

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

KO

K00135.

Pfam

PF00171. Aldedh. 1 hit.
[Graphical view]

SUPFAM

SSF53720. Aldehyde_DH/Histidinol_DH. 1 hit.

TIGRFAMs

TIGR01780. SSADH. 1 hit.

PROSITE

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

ProtoNet

Search...

Entry information

Entry name

GABD_ECOLI

Accession

Primary (citable) accession number: P25526
Secondary accession number(s): P78207, P78208, P78209

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1992
Last sequence update:	May 1, 1992
Last modified:	January 25, 2012
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program