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Title :   CRYSTAL STRUCTURE OF THE NITROGENASE FE PROTEIN ASP39ASN WITH MGADP BOUND

Authors :   S. B. Jang, M. S. Jeong, L. C. Seefeldt, J. W. Peters

Date :   05 Sep 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   [Fes] Cluster, Fe Protein, Signal Transduction, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Jang, M. S. Jeong, L. C. Seefeldt, J. W. Peters
Structural And Biochemical Implications Of Single Amino Acid Substitutions In The Nucleotide-Dependent Switch Regions Of The Nitrogenase Fe Protein From Azotobacter Vinelandii
J. Biol. Inorg. Chem. V. 9 1028 2004
PubMed-ID: 15549494 | Reference-DOI: 10.1007/S00775-004-0605-5
(for further references see the PDB file header)

Molecule 1 - NITROGENASE IRON PROTEIN 1
	Chains	:	A, B
	EC Number	:	1.18.6.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLCS586
	Expression System Strain	:	CJ236
	Expression System Taxid	:	562
	Expression System Vector	:	PTZ19U
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Synonym	:	NITROGENASE FE PROTEIN, NITROGENASE COMPONENT II, NITROGENASE REDUCTASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:15 , SER A:16 , ASP A:43 , SER A:44 , ADP A:291	BINDING SITE FOR RESIDUE MG A 293
2	AC2	SOFTWARE	SER B:16 , ASP B:43 , ADP B:292	BINDING SITE FOR RESIDUE MG B 294
3	AC3	SOFTWARE	CYS A:97 , ALA A:98 , CYS A:132 , GLY A:134 , CYS B:97 , ALA B:98 , CYS B:132 , GLY B:134 , PHE B:135	BINDING SITE FOR RESIDUE SF4 A 290
4	AC4	SOFTWARE	LYS A:10 , GLY A:11 , GLY A:12 , ILE A:13 , GLY A:14 , LYS A:15 , SER A:16 , THR A:17 , ASN A:185 , PRO A:212 , ARG A:213 , ASP A:214 , VAL A:217 , GLN A:218 , GLU A:221 , MG A:293	BINDING SITE FOR RESIDUE ADP A 291
5	AC5	SOFTWARE	LYS B:10 , GLY B:12 , ILE B:13 , GLY B:14 , LYS B:15 , SER B:16 , THR B:17 , ASN B:185 , VAL B:211 , PRO B:212 , ARG B:213 , ASP B:214 , VAL B:217 , GLU B:221 , TYR B:240 , MG B:294	BINDING SITE FOR RESIDUE ADP B 292

(no "SS Bond" information available for 1XD9)

(no "Cis Peptide Bond" information available for 1XD9)

(no "SAP(SNP)/Variant" information available for 1XD9)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NIFH_FRXC_3	PS51026	NIFH_FRXC family profile.	NIFH1_AZOVI	3-275	2	A:2-274 B:2-274
2	NIFH_FRXC_1	PS00746	NifH/frxC family signature 1.	NIFH1_AZOVI	88-100	2	A:87-99 B:87-99
3	NIFH_FRXC_2	PS00692	NifH/frxC family signature 2.	NIFH1_AZOVI	126-139	2	A:125-138 B:125-138

(no "Exon" information available for 1XD9)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:289
 aligned with NIFH1_AZOVI | P00459 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281         
          NIFH1_AZOVI     2 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV 290
               SCOP domains d1xd9a_ A: Nitrogenase iron protein                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1xd9A00 A:1-289 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh.....eeeee.......hhhhhh.....hhhhhhhhh.hhhhhhhhhh.eeehhheeeee.........hhhhhhhhhhhhhhhh........eeeeeee........hhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NIFH_FRXC_3  PDB: A:2-274 UniProt: 3-275                                                                                                                                                                                                                                         --------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------NIFH_FRXC_1  -------------------------NIFH_FRXC_2   ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xd9 A   1 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCNPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

Chain B from PDB  Type:PROTEIN  Length:289
 aligned with NIFH1_AZOVI | P00459 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281         
          NIFH1_AZOVI     2 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV 290
               SCOP domains d1xd9b_ B: Nitrogenase iron protein                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1xd9B00 B:1-289 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) --Fer4_NifH-1xd9B01 B:3-275                                                                                                                                                                                                                                                        -------------- Pfam domains (1)
           Pfam domains (2) --Fer4_NifH-1xd9B02 B:3-275                                                                                                                                                                                                                                                        -------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh.....eeeee.......hhhhhh.....hhhhhhhhh.hhhhhhhhhh.eeehhheeeee.........hhhhhhhhhhhhhhhh........eeeeeee........hhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh..eeeee...hhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NIFH_FRXC_3  PDB: B:2-274 UniProt: 3-275                                                                                                                                                                                                                                         --------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------NIFH_FRXC_1  -------------------------NIFH_FRXC_2   ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xd9 B   1 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCNPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAEEV 289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nitrogenase iron protein-like (152)

Protein domain: Nitrogenase iron protein (21)

Azotobacter vinelandii [TaxId: 354] (20)

1a	d1xd9a_	A:
1b	d1xd9b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Azotobacter vinelandii. Organism_taxid: 354. (5)

1a	1xd9A00	A:1-289
1b	1xd9B00	B:1-289

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Fer4_NifH (10)

Azotobacter vinelandii (10)

1a	Fer4_NifH-1xd9B01	B:3-275
1b	Fer4_NifH-1xd9B02	B:3-275

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NIFH1_AZOVI | P00459)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0018697	carbonyl sulfide nitrogenase activity	Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016163	nitrogenase activity	Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016612	molybdenum-iron nitrogenase complex	An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

Asymmetric/Biological Unit
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1de0	MODULATING THE MIDPOINT POTENTIAL OF THE [4FE-4S] CLUSTER OF THE NITROGENASE FE PROTEIN
1fp6	INSIGHTS INTO NUCLEOTIDE SIGNAL TRANSDUCTION IN NITROGENASE: STRUCTURE OF AN IRON PROTEIN WITH MGADP BOUND
1xd8	THE SAME PROTEIN WITH D39N MUTANT
1xdb	THE SAME PROTEIN WITH D129E MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

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