3C8Y - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   1.39 ANGSTROM CRYSTAL STRUCTURE OF FE-ONLY HYDROGENASE

Authors :   A. S. Pandey, B. J. Lemon, J. W. Peters

Date :   14 Feb 08 (Deposition) - 22 Apr 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.39

Chains :   Asym./Biol. Unit : A

Keywords :   Dithiomethylether, H-Cluster, Hydrogenase, Iron, Iron-Sulfur, Metal- Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. S. Pandey, T. V. Harris, L. J. Giles, J. W. Peters, R. K. Szilagyi
Dithiomethylether As A Ligand In The Hydrogenase H-Cluster.
J. Am. Chem. Soc. V. 130 4533 2008
PubMed-ID: 18324814 | Reference-DOI: 10.1021/JA711187E

Molecule 1 - IRON HYDROGENASE 1
	Chains	:	A
	EC Number	:	1.12.7.2
	Organism Scientific	:	CLOSTRIDIUM PASTEURIANUM
	Synonym	:	[FE] HYDROGENASE, FE-ONLY HYDROGENASE, CPI

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
2	GOL	3	Ligand/Ion	GLYCEROL
3	HCN	1	Ligand/Ion	2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHERCLUSTER
4	SF4	4	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:230 , PRO A:231 , SER A:232 , ILE A:268 , ALA A:272 , CYS A:299 , PRO A:324 , GLN A:325 , MET A:353 , PRO A:354 , CYS A:355 , LYS A:358 , PHE A:417 , MET A:497 , CYS A:503	BINDING SITE FOR RESIDUE HCN A 575
2	AC2	SOFTWARE	CYS A:300 , PRO A:301 , CYS A:355 , CYS A:499 , CYS A:503 , GLY A:506	BINDING SITE FOR RESIDUE SF4 A 576
3	AC3	SOFTWARE	CYS A:157 , THR A:163 , MET A:166 , CYS A:190 , LEU A:191 , LEU A:192 , CYS A:193 , GLY A:194 , CYS A:196	BINDING SITE FOR RESIDUE SF4 A 577
4	AC4	SOFTWARE	CYS A:147 , LEU A:148 , LEU A:149 , CYS A:150 , GLY A:151 , CYS A:153 , CYS A:200 , PRO A:201 , ALA A:204 , LEU A:205	BINDING SITE FOR RESIDUE SF4 A 578
5	AC5	SOFTWARE	HIS A:94 , GLU A:95 , PHE A:96 , LYS A:97 , CYS A:98 , CYS A:101 , CYS A:107 , LYS A:146 , ALA A:203	BINDING SITE FOR RESIDUE SF4 A 579
6	AC6	SOFTWARE	LEU A:33 , CYS A:34 , PHE A:35 , CYS A:46 , GLU A:47 , CYS A:49 , CYS A:62	BINDING SITE FOR RESIDUE FES A 580
7	AC7	SOFTWARE	LYS A:223 , LYS A:333 , LYS A:345 , PHE A:348 , ARG A:373 , ASP A:376 , HOH A:1087	BINDING SITE FOR RESIDUE GOL A 581
8	AC8	SOFTWARE	ARG A:104 , ASN A:106 , CYS A:107 , LEU A:110 , LYS A:111 , ASN A:437 , HOH A:795 , HOH A:1008	BINDING SITE FOR RESIDUE GOL A 582
9	AC9	SOFTWARE	LYS A:223 , PHE A:348 , HOH A:701 , HOH A:846 , HOH A:855	BINDING SITE FOR RESIDUE GOL A 583

(no "SS Bond" information available for 3C8Y)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:291	-	Pro A:292
2	Phe A:293	-	Pro A:294

(no "SAP(SNP)/Variant" information available for 3C8Y)

Asymmetric/Biological Unit (3, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	2FE2S_FER_2	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.	PHF1_CLOPA	1-78	1	A:1-78
2	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	PHF1_CLOPA	138-167 181-210	2	A:138-167 A:181-210
3	4FE4S_FER_1	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.	PHF1_CLOPA	147-158 190-201	2	A:147-158 A:190-201

(no "Exon" information available for 3C8Y)

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:574
 aligned with PHF1_CLOPA | P29166 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:574
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570    
           PHF1_CLOPA     1 MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKK 574
               SCOP domains d3c8ya2 A:1-126 Fe-only hydrogenase, N-terminal domain                                                                        d3c8ya3 A:127-209 Fe-only hydrogenase, second domain                               d3c8ya1 A:210-574 Fe-only hydrogenase, catalytic domain                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------3c8yA02 A:125-208  [code=3.30.70.20, no name defined]                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....hhhhhhhhh.......................eeee...eeee.hhh......eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.hhh...hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhh....hhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) 2FE2S_FER_2  PDB: A:1-78 UniProt: 1-78                                        -----------------------------------------------------------4FE4S_FER_2  PDB: A:138-167   -------------4FE4S_FER_2  PDB: A:181-210   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------4FE4S_FER_1 -------------------------------4FE4S_FER_1 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c8y A   1 MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKK 574
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.20, no name defined] (120)

Clostridium pasteurianum (1)

3c8yA02

A:125-208

(no "Pfam Domain" information available for 3C8Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PHF1_CLOPA | P29166)

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:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0008901	ferredoxin hydrogenase activity	Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:291 - Pro A:292	[ RasMol ]
		Phe A:293 - Pro A:294	[ RasMol ]

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	PHF1_CLOPA \| P29166	:	1c4a 1c4c 1feh 4xdc 4xdd 5byq 5byr 5bys 5la3

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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