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Title :   CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS

Authors :   Y. Montet, A. Volbeda, C. Piras, E. C. Hatchikian, M. Frey, J. C. Fonteci

Date :   21 Jul 98 (Deposition) - 29 Jul 98 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : L,S

Keywords :   Ni-Fe Hydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Rousset, Y. Montet, B. Guigliarelli, N. Forget, M. Asso, P. Bertrand, J. C. Fontecilla-Camps, E. C. Hatchikian
3Fe-4S] To [4Fe-4S] Cluster Conversion In Desulfovibrio Fructosovorans [Nife] Hydrogenase By Site-Directed Mutagenesis
Proc. Natl. Acad. Sci. Usa V. 95 11625 1998
PubMed-ID: 9751716 | Reference-DOI: 10.1073/PNAS.95.20.11625
(for further references see the PDB file header)

Molecule 1 - [NI-FE] HYDROGENASE
	Cellular Location	:	PERIPLASM
	Chains	:	S
	EC Number	:	1.18.99.1
	Fragment	:	SMALL CHAIN
	Organism Scientific	:	DESULFOVIBRIO FRUCTOSOVORANS
	Organism Taxid	:	878
	Other Details	:	DSM 3604
	Strain	:	WILD TYPE
	Synonym	:	CYTOCHROME C3 HYDROGENASE

Molecule 2 - [NI-FE] HYDROGENASE
	Cellular Location	:	PERIPLASM
	Chains	:	L
	EC Number	:	1.18.99.1
	Fragment	:	LARGE CHAIN
	Organism Scientific	:	DESULFOVIBRIO FRUCTOSOVORANS
	Organism Taxid	:	878
	Other Details	:	DSM 3604
	Strain	:	WILD TYPE
	Synonym	:	CYTOCHROME C3 HYDROGENASE

		1	2
Asymmetric/Biological Unit	:	L	S

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 6)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	FE	1	Ligand/Ion	FE (III) ION
3	MG	1	Ligand/Ion	MAGNESIUM ION
4	NI	1	Ligand/Ion	NICKEL (II) ION
5	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS L:75 , CYS L:546 , NI L:566 , HOH L:616 , HOH L:622	BINDING SITE FOR RESIDUE FE L 565
2	AC2	SOFTWARE	CYS L:72 , CYS L:75 , CYS L:543 , CYS L:546 , FE L:565	BINDING SITE FOR RESIDUE NI L 566
3	AC3	SOFTWARE	GLU L:53 , GLU L:334 , GLN L:494 , LEU L:495 , HIS L:549 , HOH L:632	BINDING SITE FOR RESIDUE MG L 567
4	AC4	SOFTWARE	HIS S:184 , CYS S:187 , ARG S:189 , LEU S:190 , PHE S:193 , CYS S:212 , LEU S:213 , CYS S:218 , PRO S:221 , VAL S:239	BINDING SITE FOR RESIDUE SF4 S 265
5	AC5	SOFTWARE	LYS L:225 , GLN L:230 , THR S:223 , ASN S:225 , CYS S:227 , TRP S:237 , PRO S:238 , CYS S:245 , LEU S:246 , CYS S:248	BINDING SITE FOR RESIDUE F3S S 266
6	AC6	SOFTWARE	ARG L:70 , HIS L:228 , CYS S:17 , CYS S:20 , GLY S:112 , THR S:113 , CYS S:114 , GLY S:146 , CYS S:147 , PRO S:148	BINDING SITE FOR RESIDUE SF4 S 267
7	ACT	AUTHOR	NI L:566 , FE L:565	THE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE NI ION IS COORDINATED BY TWO TERMINAL CYSTEINES CYS L 72 ? AND CYS L 543 ? AND TWO BRIDGING CYSTEINES BETWEEN FE AND NI, CYS L 75 ? AND CYS L 546 ?.

Asymmetric/Biological Unit

No.	Residues
1	L:75	-	L:546
2	L:259	-	L:436

Asymmetric/Biological Unit

No.	Residues
1	Lys S:29	-	Pro S:30
2	Lys S:124	-	Pro S:125
3	Cys S:147	-	Pro S:148
4	Asp L:19	-	Pro L:20
5	Asn L:226	-	Pro L:227

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NI_HGENASE_L_1	PS00507	Nickel-dependent hydrogenases large subunit signature 1.	PHNL_DESFR	50-75	1	L:50-75
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESFR	540-549	1	L:540-549

(no "Exon" information available for 1FRF)

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 L from PDB  Type:PROTEIN  Length:543
 aligned with PHNL_DESFR | P18188 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:543
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546   
           PHNL_DESFR     7 TPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
               SCOP domains d1frfl_ L: Nickel-iron hydrogenase, large subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1frfL00 L:7-549 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.........eeeeeeee..eeeeeeeee.....hhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee....hhhhhhhheee..eee................eee.............hhhhh...................eee......eehhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1frf L   7 TPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIDTARTGNSEKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVNLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGSLSHWIRIKGKKIDNFQLVVPSTWNLGPRGPQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546

Chain S from PDB  Type:PROTEIN  Length:261
 aligned with PHNS_DESFR | P18187 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:261
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313 
           PHNS_DESFR    54 KHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 314
               SCOP domains d1frfs_ S: Nickel-iron hydrogenase, small subunit                                                                                                                                                                                                                     SCOP domains
               CATH domains 1frfS01 S:4-178  [code=3.40.50.700, no name defined]                                                                                                                           1frfS02 S:179-263 Cytochrome-c3 Hydrogenase, chain A, domain 2                       - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhh.....hhhhhhhhh.eeee.......hhhhhhhhhhhhhhh....eeeee..ee.hhhhh..ee..eehhhhhhhhhhhh.eeeee.hhhhhh...........eehhhhhhh...eee.....hhhhhhhhhhhhhh...........hhhhhh.hhhhhh.hhhhhhh........hhhhhh.........hhhhh..hhhhhh.....hhhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1frf S   4 KHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGETSEAALHEALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETCKKAAAKAKGIICIGTCSPYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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 '\|'

(no "Pfam Domain" information available for 1FRF)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (PHNL_DESFR | P18188)

molecular function
	GO:0047806	cytochrome-c3 hydrogenase activity	Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
	GO:0008901	ferredoxin hydrogenase activity	Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	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: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:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain S (PHNS_DESFR | P18187)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	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:0047806	cytochrome-c3 hydrogenase activity	Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
	GO:0008901	ferredoxin hydrogenase activity	Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
	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: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: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:0009375	ferredoxin hydrogenase complex	An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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		Cys S:147 - Pro S:148	[ RasMol ]
		Lys S:124 - Pro S:125	[ RasMol ]
		Lys S:29 - Pro S:30	[ RasMol ]

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 6)

Sites (7, 7)

SS Bonds (2, 2)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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