1L5H - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   FEMO-COFACTOR DEFICIENT NITROGENASE MOFE PROTEIN

Authors :   B. Schmid, M. W. Ribbe, O. Einsle, M. Yoshida, L. M. Thomas, D. R. Dean, D. B. K. Burgess

Date :   06 Mar 02 (Deposition) - 17 Apr 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Apo-Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Schmid, M. W. Ribbe, O. Einsle, M. Yoshida, L. M. Thomas, D. R. Dean, D. C. Rees, B. K. Burgess
Structure Of A Cofactor-Deficient Nitrogenase Mofe Protein.
Science V. 296 352 2002
PubMed-ID: 11951047 | Reference-DOI: 10.1126/SCIENCE.1070010

Molecule 1 - NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN
	Chains	:	A
	EC Number	:	1.18.6.1
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Synonym	:	NITROGENASE MOFE PROTEIN

Molecule 2 - NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN
	Chains	:	B
	EC Number	:	1.18.6.1
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354
	Synonym	:	NITROGENASE MOFE PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CLF	1	Ligand/Ion	FE(8)-S(7) CLUSTER

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CLF	2	Ligand/Ion	FE(8)-S(7) CLUSTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:549 , ARG B:108 , GLU B:109 , ASP B:353 , ASP B:357 , HOH B:708	BINDING SITE FOR RESIDUE CA B 601
2	AC2	SOFTWARE	CYS A:62 , TYR A:64 , CYS A:88 , CYS A:154 , GLY A:185 , CYS B:70 , PRO B:72 , SER B:92 , GLY B:94 , CYS B:95 , TYR B:98 , THR B:152 , CYS B:153 , SER B:188	BINDING SITE FOR RESIDUE CLF B 602

(no "SS Bond" information available for 1L5H)

Asymmetric Unit

No.	Residues
1	Gly A:448	-	Pro A:449
2	Tyr B:12	-	Pro B:13
3	Phe B:471	-	Pro B:472

(no "SAP(SNP)/Variant" information available for 1L5H)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NITROGENASE_1_1	PS00699	Nitrogenases component 1 alpha and beta subunits signature 1.	NIFD_AZOVI	81-88	1	A:81-88
1	NITROGENASE_1_1	PS00699		NIFK_AZOVI	88-95	1	B:88-95
2	NITROGENASE_1_2	PS00090	Nitrogenases component 1 alpha and beta subunits signature 2.	NIFK_AZOVI	151-165	1	B:151-165
2	NITROGENASE_1_2	PS00090		NIFD_AZOVI	152-166	1	A:152-166

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NITROGENASE_1_1	PS00699	Nitrogenases component 1 alpha and beta subunits signature 1.	NIFD_AZOVI	81-88	2	A:81-88
1	NITROGENASE_1_1	PS00699		NIFK_AZOVI	88-95	2	B:88-95
2	NITROGENASE_1_2	PS00090	Nitrogenases component 1 alpha and beta subunits signature 2.	NIFK_AZOVI	151-165	2	B:151-165
2	NITROGENASE_1_2	PS00090		NIFD_AZOVI	152-166	2	A:152-166

(no "Exon" information available for 1L5H)

Asymmetric 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:405
 aligned with NIFD_AZOVI | P07328 from UniProtKB/Swiss-Prot  Length:492

    Alignment length:432
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478  
           NIFD_AZOVI    49 NKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
               SCOP domains d1l5ha_ A: Nitrogenase iron-molybdenum protein, alpha chain                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -1l5hA01 A:50-208 Nitrogenase molybdenum iron protein domain                                                                                                    1l5hA03 A:209-319 Nitrogenase molybdenum iron protein domain                                                   -------------------------1l5hA02 A:345-480 Nitrogenase molybd                           enum iron protein domain                                                  CATH domains
               Pfam domains -------------Oxidored_nitro-1l5hA01 A:62-468                                                                                                                                                                                                                                                                                                                                                                                        ------------ Pfam domains
         Sec.struct. author .............hhhhhhh..........eeeee..hhhhhhhh....................ee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhh..hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee............hhhhhh..eee.....---------------------------.hhhhhhhhh..ee.....hhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------NITROGEN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------NITROGENASE_1_2-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l5h A  49 NKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYE---------------------------EFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 |       -         -       408       418       428       438       448       458       468       478  
                                                                                                                                                                                                                                                                                                                                                                     380                         408

Chain B from PDB  Type:PROTEIN  Length:522
 aligned with NIFK_AZOVI | P07329 from UniProtKB/Swiss-Prot  Length:523

    Alignment length:522
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521  
           NIFK_AZOVI     2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
               SCOP domains d1l5hb_ B: Nitrogenase iron-molybdenum protein, beta chain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------1l5hB01 B:70-215 Nitrogenase molybdenum iron protein domain                                                                                       1l5hB02 B:216-320 Nitrogenase molybdenum iron protein domain                                             1l5hB04 B:321-364,B:485-523                 1l5hB03 B:365-470 Nitrogenase molybdenum iron protein domain                                              --------------1l5hB04 B:321-364,B:485-523             CATH domains
               Pfam domains DUF3364-1l5hB01 B:2-56                                 -------------Oxidored_nitro-1l5hB02 B:70-502                                                                                                                                                                                                                                                                                                                                                                                                                  --------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhh....ee.....hhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.hhhhh.......eeee.....hhhhhhhhhhhhh.....eee.....hhhhh.............hhhhhhhhhhh.eeee.hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhh.......eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------NITROGEN-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------NITROGENASE_1_2---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1l5h B   2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Nitrogenase molybdenum iron protein domain (45)

Azotobacter vinelandii. Organism_taxid: 354. (3)

1a	1l5hA01	A:50-208
1b	1l5hB01	B:70-215
1c	1l5hA03	A:209-319
1d	1l5hB03	B:365-470
1e	1l5hB02	B:216-320
1f	1l5hA02	A:345-480

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 (19)

Homologous Superfamily: Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 (19)

Azotobacter vinelandii. Organism_taxid: 354. (3)

1l5hB04

B:321-364,B:485-523

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF3364] (10)

Family: DUF3364 (10)

Azotobacter vinelandii (8)

DUF3364-1l5hB01

B:2-56

Clan: no clan defined [family: Oxidored_nitro] (12)

Family: Oxidored_nitro (12)

Azotobacter vinelandii (8)

2a	Oxidored_nitro-1l5hA01	A:62-468
2b	Oxidored_nitro-1l5hB02	B:70-502

Asymmetric Unit(hide GO term definitions)

Chain A (NIFD_AZOVI | P07328)

molecular function
	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.

Chain B (NIFK_AZOVI | P07329)

molecular function
	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 Unit
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		Phe B:471 - Pro B:472	[ RasMol ]
		Tyr B:12 - Pro B:13	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1L5H)

Description

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Ligands, Modified Residues, Ions (2, 2)

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