Nitrogenase molybdenum-iron protein alpha chain

Contribute

Send feedback

Read comments (?) or add your own

P07328 (NIFD_AZOVI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 96. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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

Azotobacter vinelandii

Taxonomic identifier

354 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Azotobacter

Protein attributes

Sequence length	492 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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.

Ontologies

Keywords
Biological process	Nitrogen fixation
Ligand	ATP-binding Iron Iron-sulfur Metal-binding Molybdenum Nucleotide-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
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

Initiator methionine

Removed Ref.4

Chain

2 – 492

491

Nitrogenase molybdenum-iron protein alpha chain

PRO_0000153058

Sites

Metal binding

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

Metal binding

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

Metal binding

154

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

Metal binding

275

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

Metal binding

442

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

Experimental info

Mutagenesis

195

H → Q: No nitrogenase activity.

Sequence conflict

G → R in AAA22143. Ref.3

Sequence conflict

190

S → C in AAA22143. Ref.3

Sequence conflict

212

E → A in AAA22143. Ref.3

Sequence conflict

258 – 261

SISE → YISQ Ref.3

Sequence conflict

407

Y → M in AAA22143. Ref.3

Sequence conflict

440

E → Q Ref.1

Sequence conflict

440

E → Q Ref.3

Secondary structure

492

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P07328 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 7D4B2CF5E99664D7
Show »

FASTA

492

55,289

        10         20         30         40         50         60 
MTGMSREEVE SLIQEVLEVY PEKARKDRNK HLAVNDPAVT QSKKCIISNK KSQPGLMTIR 

        70         80         90        100        110        120 
GCAYAGSKGV VWGPIKDMIH ISHGPVGCGQ YSRAGRRNYY IGTTGVNAFV TMNFTSDFQE 

       130        140        150        160        170        180 
KDIVFGGDKK LAKLIDEVET LFPLNKGISV QSECPIGLIG DDIESVSKVK GAELSKTIVP 

       190        200        210        220        230        240 
VRCEGFRGVS QSLGHHIAND AVRDWVLGKR DEDTTFASTP YDVAIIGDYN IGGDAWSSRI 

       250        260        270        280        290        300 
LLEEMGLRCV AQWSGDGSIS EIELTPKVKL NLVHCYRSMN YISRHMEEKY GIPWMEYNFF 

       310        320        330        340        350        360 
GPTKTIESLR AIAAKFDESI QKKCEEVIAK YKPEWEAVVA KYRPRLEGKR VMLYIGGLRP 

       370        380        390        400        410        420 
RHVIGAYEDL GMEVVGTGYE FAHNDDYDRT MKEMGDSTLL YDDVTGYEFE EFVKRIKPDL 

       430        440        450        460        470        480 
IGSGIKEKFI FQKMGIPFRE MHSWDYSGPY HGFDGFAIFA RDMDMTLNNP CWKKLQAPWE 

       490 
ASEGAEKVAA SA

« Hide

References

[1]	"Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii." Jacobson M.R., Brigle K.E., Bennett L.T., Setterquist R.A., Wilson M.S., Cash V.L., Beynon J., Newton W.E., Dean D.R. J. Bacteriol. 171:1017-1027(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Sequence of a 1.4 kb Eco RI fragment of Azotobacter vinelandii nif DNA." Hiratsuka K., Roy K.L. Nucleic Acids Res. 16:1207-1207(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-409. Strain: ATCC 13705 / OP1 / DSM 366 / NCIB 11614 / LMG 3878 / UW.
[3]	"Complete nucleotide sequence of the Azotobacter vinelandii nitrogenase structural gene cluster." Brigle K.E., Newton W.E., Dean D.R. Gene 37:37-44(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"Isolation and partial characterization of two different subunits from the molybdenum-iron protein of Azotobacter vinelandii nitrogenase." Lundell D.J., Howard J.B. J. Biol. Chem. 253:3422-3426(1978) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-20.
[5]	"Crystallographic structure and functional implications of the nitrogenase molybdenum-iron protein from Azotobacter vinelandii." Kim J., Rees D.C. Nature 360:553-560(1992) Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
[6]	"Structure of ADP x [AlF(4)](-)-stabilized nitrogenase complex and its implications for signal transduction." Schindelin H., Kisker C., Schlessman J.L., Howard J.B., Rees D.C. Nature 387:370-376(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS).
[7]	"Redox-dependent structural changes in the nitrogenase P-cluster." Peters J.W., Stowell M.H.B., Soltis S.M., Finnegan M.G., Johnson M.K., Rees D.C. Biochemistry 36:1181-1187(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
[8]	"MgATP-bound and nucleotide-free structures of a nitrogenase protein complex between the Leu 127Delta-Fe-protein and the MoFe-protein." Chiu H.-J., Peters J.W., Lanzilotta W.N., Ryle M.J., Seefeldt L.C., Howard J.B., Rees D.C. Biochemistry 40:641-650(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
[9]	"Mechanistic features and structure of the nitrogenase alpha-Gln195 MoFe protein." Soerlie M., Christiansen J., Lemon B.J., Peters J.W., Dean D.R., Hales B.J. Biochemistry 40:1540-1549(2001) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF MUTANT GLN-195.
[10]	"Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP-AlF4(-)-stabilized structure." Schmid B., Einsle O., Chiu H.J., Willing A., Yoshida M., Howard J.B., Rees D.C. Biochemistry 41:15557-15565(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF CROSS-LINKED HETERODIMER WITH FE-PROTEIN.
[11]	"Structure of a cofactor-deficient nitrogenase MoFe protein." Schmid B., Ribbe M.W., Einsle O., Yoshida M., Thomas L.M., Dean D.R., Rees D.C., Burgess B.K. Science 296:352-356(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
[12]	"Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor." Einsle O., Tezcan F.A., Andrade S.L.A., Schmid B., Yoshida M., Howard J.B., Rees D.C. Science 297:1696-1700(2002) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.16 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M20568 Genomic DNA. Translation: AAA64710.1.
M11579 Genomic DNA. Translation: AAA22143.1.
X06886 Genomic DNA. Translation: CAA30004.1.

PIR

NIAVMA. A43049.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1FP4	X-ray	2.50	A/C	1-492	[»]
1G20	X-ray	2.20	A/C	1-492	[»]
1G21	X-ray	3.00	A/C	1-492	[»]
1L5H	X-ray	2.30	A	2-492	[»]
1M1N	X-ray	1.16	A/C/E/G	2-492	[»]
1M1Y	X-ray	3.20	A/C/I/K	2-492	[»]
1M34	X-ray	2.30	A/C/I/K	2-492	[»]
1N2C	X-ray	3.00	A/C	2-492	[»]
2AFH	X-ray	2.10	A/C	2-491	[»]
2AFI	X-ray	3.10	A/C/I/K	2-491	[»]
2AFK	X-ray	2.30	A/C	2-491	[»]
2MIN	X-ray	2.03	A/C	2-492	[»]
3K1A	X-ray	2.23	A/C	2-492	[»]
3MIN	X-ray	2.03	A/C	2-492	[»]
3U7Q	X-ray	1.00	A/C	1-492	[»]

ProteinModelPortal

P07328.

SMR

P07328. Positions 4-481.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-6252N.

MINT

MINT-1508543.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-16520.

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

P07328.

Entry information

Entry name

NIFD_AZOVI

Accession

Primary (citable) accession number: P07328

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 96 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents