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Title :   THREE-DIMENSIONAL STRUCTURE OF THE CARBON MONOXIDE COMPLEX OF [NIFE]HYDROGENASE FROM DESULUFOVIBRIO VULGARIS MIYAZAKI F

Authors :   H. Ogata, Y. Mizoguchi, N. Mizuno, K. Miki, S. Adachi, N. Yasuoka, T. Yagi, O. Yamauchi, S. Hirota, Y. Higuchi

Date :   04 Apr 03 (Deposition) - 29 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   High Resolution Crystal Structure, [Nife]Hydrogenase, Oxidoreductase, Carbon Monoxide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Ogata, Y. Mizoguchi, N. Mizuno, K. Miki, S. Adachi, N. Yasuoka, T. Yagi, O. Yamauchi, S. Hirota, Y. Higuchi
Structural Studies Of The Carbon Monoxide Complex Of [Nife]Hydrogenase From Desulfovibrio Vulgaris Miyazaki F: Suggestion For The Initial Activation Site For Dihydrogen
J. Am. Chem. Soc. V. 124 11628 2002
PubMed-ID: 12296727 | Reference-DOI: 10.1021/JA012645K
(for further references see the PDB file header)

Molecule 1 - PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
	Chains	:	S
	EC Number	:	1.12.2.1
	Organism Scientific	:	DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
	Organism Taxid	:	883
	Strain	:	MIYAZAKI F
	Synonym	:	SMALL SUBUNIT OF [NIFE]HYDROGENASE

Molecule 2 - PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
	Chains	:	L
	EC Number	:	1.12.2.1
	Fragment	:	RESIDUES 19-552
	Organism Scientific	:	DESULFOVIBRIO VULGARIS STR. 'MIYAZAKI F'
	Organism Taxid	:	883
	Strain	:	MIYAZAKI F
	Synonym	:	LARGE SUBUNIT OF [NIFE]HYDROGENASE

		1	2
Asymmetric/Biological Unit	:	L	S

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	CMO	1	Ligand/Ion	CARBON MONOXIDE
2	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
3	FNE	1	Ligand/Ion	(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
4	MG	1	Ligand/Ion	MAGNESIUM ION
5	MPD	5	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU L:62 , LEU L:498 , HIS L:552 , HOH L:3001 , HOH L:3002 , HOH L:3003	BINDING SITE FOR RESIDUE MG L 1005
02	AC2	SOFTWARE	ARG L:79 , HIS L:235 , GLU S:16 , CYS S:17 , CYS S:20 , THR S:113 , CYS S:114 , GLY S:149 , CYS S:150 , PRO S:151	BINDING SITE FOR RESIDUE SF4 S 1001
03	AC3	SOFTWARE	HIS S:188 , CYS S:191 , ARG S:193 , LEU S:194 , CYS S:216 , LEU S:217 , CYS S:222	BINDING SITE FOR RESIDUE SF4 S 1002
04	AC4	SOFTWARE	LYS L:232 , GLN L:237 , THR S:227 , ASN S:229 , CYS S:231 , PHE S:236 , TRP S:241 , CYS S:249 , ILE S:250 , CYS S:252	BINDING SITE FOR RESIDUE F3S S 1003
05	AC5	SOFTWARE	CYS L:81 , CYS L:84 , HIS L:88 , ALA L:477 , PRO L:478 , ARG L:479 , LEU L:482 , VAL L:500 , PRO L:501 , SER L:502 , CYS L:546 , CYS L:549 , CMO L:1006	BINDING SITE FOR RESIDUE FNE L 1004
06	AC6	SOFTWARE	CYS L:81 , VAL L:83 , CYS L:84 , ARG L:479 , CYS L:546 , FNE L:1004	BINDING SITE FOR RESIDUE CMO L 1006
07	AC7	SOFTWARE	MET L:379 , LEU S:194 , ASP S:198 , HOH S:3404 , HOH S:3777	BINDING SITE FOR RESIDUE MPD S 2001
08	AC8	SOFTWARE	ASN S:134 , ASN S:146 , HOH S:3119 , HOH S:3573 , HOH S:3590	BINDING SITE FOR RESIDUE MPD S 2004
09	AC9	SOFTWARE	PHE L:324 , LEU L:392 , TYR L:395 , SER L:396 , PRO L:417 , PHE L:421	BINDING SITE FOR RESIDUE MPD L 2006
10	BC1	SOFTWARE	HIS S:68 , GLY S:69 , PHE S:70 , TYR S:164	BINDING SITE FOR RESIDUE MPD S 2007
11	BC2	SOFTWARE	GLU L:348 , TRP L:463 , MET L:465 , HOH L:3336 , HOH L:3790	BINDING SITE FOR RESIDUE MPD L 2010

Asymmetric/Biological Unit

No.	Residues
1	L:84	-	L:549

Asymmetric/Biological Unit

No.	Residues
1	Glu S:29	-	Pro S:30
2	Lys S:124	-	Pro S:125
3	Cys S:150	-	Pro S:151
4	Thr S:262	-	Pro S:263
5	Asp L:28	-	Pro L:29
6	Asn L:233	-	Pro L:234

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

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_DESVM	59-84	1	L:59-84
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESVM	543-552	1	L:543-552

(no "Exon" information available for 1UBL)

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:534
 aligned with PHNL_DESVM | P21852 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:534
                                    28        38        48        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       488       498       508       518       528       538       548    
           PHNL_DESVM    19 SSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVESGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVH 552
               SCOP domains d1ubll_ L: Nickel-iron hydrogenase, large subunit                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1ublL00 L:19-552 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....hhh.eeeeeeee...........hhh.eeee............hhhhh.........hhhhh.....eeee.......hhhhhhhhhhhh.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
                 1ubl L  19 SSYSGPIVVDPVTRIEGHLRIEVEVENGKVKNAYSSSTLFRGLEIILKGRDPRDAQHFTQRTCGVCTYTHALASTRCVDNAVGVHIPKNATYIRNLVLGAQYLHDHIVHFYHLHALDFVDVTAALKADPAKAAKVASSISPRKTTAADLKAVQDKLKTFVETGQLGPFTNAYFLGGHPAYYLDPETNLIATAHYLEALRLQVKAARAMAVFGAKNPHTQFTVVGGVTCYDALTPQRIAEFEALWKETKAFVDEVYIPDLLVVAAAYKDWTQYGGTDNFITFGEFPKDEYDLNSRFFKPGVVFKRDFKNIKPFDKMQIEEHVRHSWYEGAEARHPWKGQTQPKYTDLHGDDRYSWMKAPRYMGEPMETGPLAQVLIAYSQGHPKVKAVTDAVLAKLGVGPEALFSTLGRTAARGIETAVIAEYVGVMLQEYKDNIAKGDNVICAPWEMPKQAEGVGFVNAPRGGLSHWIRIEDGKIGNFQLVVPSTWTLGPRCDKNKLSPVEASLIGTPVADAKRPVEILRTVHSFDPCIACGVH 552
                                    28        38        48        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       488       498       508       518       528       538       548

Chain S from PDB  Type:PROTEIN  Length:267
 aligned with PHNS_DESVM | P21853 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:267
                                    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       
           PHNS_DESVM    51 LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN 317
               SCOP domains d1ubls_ S: Nickel-iron hydrogenase, small subunit                                                                                                                                                                                                                           SCOP domains
               CATH domains --1ublS01 S:3-182  [code=3.40.50.700, no name defined]                                                                                                                                1ublS02 S:183-267 Cytochrome-c3 Hydrogenase, chain A, domain 2                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhh....hhhhhhhh..eeee.......hhhhhhhhhhhhhh.....eeeee..ee.hhhhh..ee..eehhhhhhhhhhhh.eeeeehhhhhhhhhhhh......eehhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhh........hhhhhh...hhhhh.hhhhh..hhhhhh......hhhhh.........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ubl S   1 LMGPRRPSVVYLHNAECTGCSESVLRAFEPYIDTLILDTLSLDYHETIMAAAGDAAEAALEQAVNSPHGFIAVVEGGIPTAANGIYGKVANHTMLDICSRILPKAQAVIAYGTCATFGGVQAAKPNPTGAKGVNDALKHLGVKAINIAGCPPNPYNLVGTIVYYLKNKAAPELDSLNRPTMFFGQTVHEQCPRLPHFDAGEFAPSFESEEARKGWCLYELGCKGPVTMNNCPKIKFNQTNWPVDAGHPCIGCSEPDFWDAMTPFYQN 267
                                    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

Legend:		→ Mismatch	(orange background)
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	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 1UBL)

Asymmetric/Biological Unit(hide GO term definitions)

Chain L (PHNL_DESVM | P21852)

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_DESVM | P21853)

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
		Asn L:233 - Pro L:234	[ RasMol ]
		Asp L:28 - Pro L:29	[ RasMol ]
		Cys S:150 - Pro S:151	[ RasMol ]
		Glu S:29 - Pro S:30	[ RasMol ]
		Lys S:124 - Pro S:125	[ RasMol ]
		Thr S:262 - Pro S:263	[ RasMol ]

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	1.12.2.1
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1ubh	1UBH CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE DARK CONDITION AT 1.35 ANGSTROM
1ubj	1UBJ CONTAINS DATA WAS COLLECTED BY HYDROGEN ATMOSPHERE IN THE DARK CONDITION
1ubk	1UBK CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE DARK CONDITION AT 1.9 ANGSTROM
1ubm	1UBM CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE STRONG LIGHT AT 1.50 ANGSTROM
1ubo	1UBO CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE DARK.
1ubr	1UBR CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE WEAK LIGHT AT 1.34 ANGSTROM
1ubt	1UBT CONTAINS DATA WAS COLLECTED BY CO ATMOSPHERE IN THE STRONG LIGHT AT 1.34 ANGSTROM
1ubu	1UBU CONTAINS DATA WAS COLLECTED BY HYDROGEN ATMOSPHERE IN THE STRONG LIGHT.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (11, 11)

SS Bonds (1, 1)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (0, 0)

Gene Ontology (11, 17)

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