P00466 (NIFD_KLEPN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Nitrogenase molybdenum-iron protein alpha chain
EC=1.18.6.1

Alternative name(s):
Dinitrogenase
Nitrogenase component I

Gene names

Name:

nifD

Organism

Klebsiella pneumoniae

Taxonomic identifier

573 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	483 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
Catalytic activity	8 reduced ferredoxin + 8 H+ + N2 + 16 ATP + 16 H2O = 8 oxidized ferredoxin + H2 + 2 NH3 + 16 ADP + 16 phosphate.
Cofactor	Binds 1 8Fe-7S cluster per heterodimer. Binds 1 7Fe-Mo-9S-X-homocitryl cluster per subunit. The identity of the X atom is not known, possibly carbon or oxygen.
Subunit structure	Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2).
Sequence similarities	Belongs to the NifD/NifK/NifE/NifN family.
Caution	The authors of Ref.6 originally stated that their sequence was from Frankia sp.

Ontologies

Keywords
Biological process	Nitrogen fixation
Ligand	ATP-binding Iron Iron-sulfur Metal-binding Molybdenum Nucleotide-binding
Molecular function	Oxidoreductase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	nitrogen fixation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	molybdenum-iron nitrogenase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW carbonyl sulfide nitrogenase activity Inferred from electronic annotation. Source: EC iron-sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nitrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 483

483

Nitrogenase molybdenum-iron protein alpha chain

PRO_0000153069

Sites

Metal binding

63

1

Iron-sulfur (8Fe-7S); shared with beta chain

Metal binding

89

1

Iron-sulfur (8Fe-7S); shared with beta chain

Metal binding

155

1

Iron-sulfur (8Fe-7S); shared with beta chain

Metal binding

275

1

Molybdenum-iron-sulfur (7Fe-Mo-9S-X-homocitryl)

Metal binding

442

1

Molybdenum-iron-sulfur (7Fe-Mo-9S-X-homocitryl); via pros nitrogen

Experimental info

Sequence conflict

16

1

E → Q Ref.4

Sequence conflict

261 – 264

4

EMEN → GDGD in CAA31179. Ref.6

Sequence conflict

288

1

E → D in CAA31179. Ref.6

Sequence conflict

341 – 343

3

KYR → NIA in CAA31179. Ref.6

Sequence conflict

349 – 361

13

RKVLL…GLRPR → LRCCSIWRLP in CAA31179. Ref.6

Sequence conflict

355

1

M → I in CAA31667. Ref.2

Sequence conflict

469

1

N → T in CAA31179. Ref.6

Secondary structure

1

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483

Helix Strand Turn

Details...

Helix

5 – 18

14

Helix

23 – 29

7

Helix

30 – 32

3

Beta strand

33 – 35

3

Helix

44 – 46

3

Helix

64 – 68

5

Helix

69 – 73

5

Beta strand

79 – 87

9

Helix

88 – 92

5

Turn

93 – 95

3

Turn

105 – 107

3

Helix

121 – 126

6

Helix

129 – 142

14

Beta strand

147 – 153

7

Helix

156 – 159

4

Helix

164 – 175

12

Beta strand

179 – 182

4

Beta strand

188 – 191

4

Helix

192 – 206

15

Turn

207 – 213

7

Beta strand

222 – 228

7

Turn

232 – 235

4

Helix

236 – 244

9

Beta strand

248 – 254

7

Helix

259 – 264

6

Helix

265 – 267

3

Beta strand

269 – 274

6

Helix

276 – 290

15

Beta strand

294 – 296

3

Helix

301 – 313

13

Helix

318 – 346

29

Beta strand

350 – 358

9

Helix

359 – 362

4

Helix

364 – 369

6

Beta strand

373 – 381

9

Helix

384 – 390

7

Helix

391 – 393

3

Beta strand

399 – 403

5

Helix

406 – 416

11

Beta strand

419 – 423

5

Helix

425 – 433

9

Beta strand

438 – 443

6

Helix

444 – 446

3

Helix

452 – 467

16

Helix

470 – 473

4

Sequences

	Sequence		Length	Mass (Da)
	P00466 [UniParc]. Last modified July 1, 1989. Version 2. Checksum: 4A2BA83B2C0C6EE7	FASTA	483	54,158
	10 20 30 40 50 60 MMTNATGERN LALIQEVLEV FPETARKERR KHMMVSDPKM KSVGKCIISN RKSQPGVMTV 70 80 90 100 110 120 RGCAYAGSKG VVFGPIKDMA HISHGPAGCG QYSRAERRNY YTGVSGVDSF GTLNFTSDFQ 130 140 150 160 170 180 ERDIVFGGDK KLSKLIEEME LLFPLTKGIT IQSECPVGLI GDDISAVANA SSKALDKPVI 190 200 210 220 230 240 PVRCEGFRGV SQSLGHHIAN DVVRDWILNN REGQPFETTP YDVAIIGDYN IGGDAWASRI 250 260 270 280 290 300 LLEEMGLRVV AQWSGDGTLV EMENTPFVKL NLVHCYRSMN YIARHMEEKH QIPWMEYNFF 310 320 330 340 350 360 GPTKIAESLR KIADQFDDTI RANAEAVIAR YEGQMAAIIA KYRPRLEGRK VLLYMGGLRP 370 380 390 400 410 420 RHVIGAYEDL GMEIIAAGYE FAHNDDYDRT LPDLKEGTLL FDDASSYELE AFVKALKPDL 430 440 450 460 470 480 IGSGIKEKYI FQKMGVPFRQ MHSWDYSGPY HGYDGFAIFA RDMDMTLNNP AWNELTAPWL KSA

References

[1]	"Nucleotide sequence of a 24,206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster of Klebsiella pneumoniae." Arnold W., Rump A., Klipp W., Priefer U.B., Puehler A. J. Mol. Biol. 203:715-738(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Arnold W. Submitted (JAN-1989) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Nucleotide and deduced amino acid sequences of the Klebsiella pneumoniae nifK gene coding for the beta-subunit of nitrogenase MoFe protein." Steinbauer J., Wenzel W., Hess D. Nucleic Acids Res. 16:7199-7199(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Nucleotide sequence of the Klebsiella pneumoniae nifD gene and predicted amino acid sequence of the alpha-subunit of nitrogenase MoFe protein." Ioannidis I., Buck M. Biochem. J. 247:287-291(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: MSAL.
[5]	"Biological nitrogen fixation: primary structure of the Klebsiella pneumoniae nifH and nifD genes." Scott K.F., Rolfe B.G., Shine J. J. Mol. Appl. Genet. 1:71-81(1981) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-207. Strain: UNF 841.
[6]	"Nucleotide sequence of nifK and partial sequence of nifD from Frankia species strain FaC1." Lignon J.M., Nakas J.P. Nucleic Acids Res. 16:11843-11843(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 207-483.
[7]	Erratum Lignon J.M., Nakas J.P. Nucleic Acids Res. 18:1097-1097(1990) Cited for: CORRECTION OF ORGANISM GIVEN IN PUBMED:3211766.
[8]	"A quantitative approach to sequence comparisons of nitrogenase MoFe protein alpha- and beta-subunits including the newly sequenced nifK gene from Klebsiella pneumoniae." Holland D., Zilberstein A., Zamir A., Sussman J.L. Biochem. J. 247:277-285(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 452-483.
[9]	"New insights into structure-function relationships in nitrogenase: a 1.6 A resolution X-ray crystallographic study of Klebsiella pneumoniae MoFe-protein." Mayer S.M., Lawson D.M., Gormal C.A., Roe S.M., Smith B.E. J. Mol. Biol. 292:871-891(1999) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 3-480.
[10]	"Crystallographic analysis of the MoFe protein of nitrogenase from a nifV mutant of Klebsiella pneumoniae identifies citrate as a ligand to the molybdenum of iron molybdenum cofactor (FeMoco)." Mayer S.M., Gormal C.A., Smith B.E., Lawson D.M. J. Biol. Chem. 277:35263-35266(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 3-483.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y00316 Genomic DNA. Translation: CAA68413.1.
X07748 Genomic DNA. Translation: CAA30571.1.
X13303 Genomic DNA. Translation: CAA31667.1.
V00631 Genomic DNA. Translation: CAA23904.1.
X12649 Genomic DNA. Translation: CAA31179.1.
X06243 Genomic DNA. Translation: CAA29587.1.

PIR

NIKBMA. S01729.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H1L	X-ray	1.90	A/C	3-483	[»]
1QGU	X-ray	1.60	A/C	3-480	[»]
1QH1	X-ray	1.60	A/C	3-480	[»]
1QH8	X-ray	1.60	A/C	3-480	[»]

ProteinModelPortal

P00466.

SMR

P00466. Positions 3-480.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6206N.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:NIFDKLEB-MONOMER.

Family and domain databases

InterPro

IPR000510. Nase/OxRdtase_comp1.
IPR010143. Nase_comp1_asu.
IPR000318. Nase_comp1_CS.
IPR005972. Nase_Mo-Fe_asu.
[Graphical view]

Pfam

PF00148. Oxidored_nitro. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01862. N2-ase-Ialpha. 1 hit.
TIGR01282. nifD. 1 hit.

PROSITE

PS00699. NITROGENASE_1_1. 1 hit.
PS00090. NITROGENASE_1_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P00466.

Entry information

Entry name

NIFD_KLEPN

Accession

Primary (citable) accession number: P00466
Secondary accession number(s): P09770

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 1, 1989
Last modified:	April 3, 2013
This is version 96 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program