3ZE9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   3D STRUCTURE OF THE NIFESE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE OXIDIZED AS-ISOLATED STATE AT 1.33 ANGSTROMS

Authors :   M. C. Marques, R. Coelho, I. A. C. Pereira, P. M. Matias

Date :   03 Dec 12 (Deposition) - 12 Jun 13 (Release) - 05 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.33

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

Keywords :   Oxidoreductase, Hydrogenase Biohydrogen Oxygen Tolerance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. Marques, R. Coelho, I. A. C. Pereira, P. M. Matias
Redox State-Dependent Changes In The Crystal Structure Of [Nifese] Hydrogenase From Desulfovibrio Vulgaris Hildenborough
Int. J. Hydrogen Energy V. 38 8664 2013
PubMed: search | Reference-DOI: 10.1016/J.IJHYDENE.2013.04.132
(for further references see the PDB file header)

Molecule 1 - PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
	Chains	:	A
	EC Number	:	1.12.7.2
	Fragment	:	RESIDUES 35-317
	Organism Scientific	:	DESULFOVIBRIO VULGARIS
	Organism Taxid	:	882
	Strain	:	HILDENBOROUGH

Molecule 2 - PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
	Chains	:	B
	EC Number	:	1.12.7.2
	Fragment	:	RESIDUES 12-495
	Organism Scientific	:	DESULFOVIBRIO VULGARIS
	Organism Taxid	:	882
	Strain	:	HILDENBOROUGH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (9, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
3	FCO	1	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
4	FE2	1	Ligand/Ion	FE (II) ION
5	FSX	1	Ligand/Ion	BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
6	NI	1	Ligand/Ion	NICKEL (II) ION
7	OCS	1	Mod. Amino Acid	CYSTEINE-S-DIOXIDE
8	PSW	1	Mod. Amino Acid	3-(SULFANYLSELANYL)-L-ALANINE
9	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , CYS A:232 , ARG A:233 , CYS A:238 , VAL A:260	BINDING SITE FOR RESIDUE SF4 A 284
2	AC2	SOFTWARE	THR A:243 , CYS A:247 , TRP A:252 , CYS A:259 , CYS A:265 , ILE A:266 , CYS A:268 , ARG B:182 , GLN B:187	BINDING SITE FOR RESIDUE SF4 A 285
3	AC3	SOFTWARE	GLY A:17 , CYS A:18 , THR A:19 , GLY A:20 , CSS A:21 , GLU A:77 , GLY A:78 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , HOH A:2112 , HIS B:185	BINDING SITE FOR RESIDUE FSX A 286
4	AC4	SOFTWARE	CYS B:78 , ALA B:420 , PRO B:421 , ARG B:422 , LEU B:425 , ALA B:444 , SER B:445 , PSW B:489 , CYS B:492 , NI B:501	BINDING SITE FOR RESIDUE FCO B 500
5	AC5	SOFTWARE	OCS B:75 , CYS B:78 , PSW B:489 , CYS B:492 , FCO B:500	BINDING SITE FOR RESIDUE NI B 501
6	AC6	SOFTWARE	GLU B:56 , ILE B:441 , HIS B:495 , HOH B:2053 , HOH B:2054 , HOH B:2286	BINDING SITE FOR RESIDUE FE2 B 502
7	AC7	SOFTWARE	CYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421	BINDING SITE FOR RESIDUE CL B 504

(no "SS Bond" information available for 3ZE9)

Asymmetric/Biological Unit

No.	Residues
1	His A:30	-	Pro A:31
2	Cys A:159	-	Pro A:160
3	Phe A:273	-	Pro A:274
4	Ser A:278	-	Pro A:279
5	Asp B:22	-	Pro B:23
6	Ala B:137	-	Pro B:138
7	Val B:140	-	Pro B:141
8	Met B:183	-	Pro B:184

(no "SAP(SNP)/Variant" information available for 3ZE9)

(no "PROSITE Motif" information available for 3ZE9)

(no "Exon" information available for 3ZE9)

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:279
 aligned with Q72AS4_DESVH | Q72AS4 from UniProtKB/TrEMBL  Length:317

    Alignment length:279
                                    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         
         Q72AS4_DESVH    39 GERPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA 317
               SCOP domains d3ze9a_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhh....hhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh...eeeeee..ee.hhhhh..eeeee..eeeehhhhhhhhh..eeeeeeehhhhhhhhhhhh......eehhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..hhhhh.hhhhhhhh............hhhhh.hhhhh..hhhhhh......hhhhhh..........hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ze9 A   5 GERPPVFWLQGQGCTGcSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA 283
                                    14      | 24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274         
                                           21-CSS

Chain B from PDB  Type:PROTEIN  Length:481
 aligned with Q72AS3_DESVH | Q72AS3 from UniProtKB/TrEMBL  Length:510

    Alignment length:481
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494 
         Q72AS3_DESVH    15 GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRICGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPULGCAVH 495
               SCOP domains d3ze9b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........eeeeeeee..eeeeeeeee....hhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..eee.......eee..eeee..eee..hhh.eeee......hhhhh..hhhhh................eeee.......hhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhh...........hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ze9 B  15 GRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRIcGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPxLGCAVH 495
                                    24        34        44        54        64        74|       84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484    |  494 
                                                                                       75-OCS                                                                                                                                                                                                                                                                                                                                                                                                                       489-PSW

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 "CATH Domain" information available for 3ZE9)

(no "Pfam Domain" information available for 3ZE9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q72AS4_DESVH | Q72AS4)

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: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.

Chain B (Q72AS3_DESVH | Q72AS3)

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: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: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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala B:137 - Pro B:138	[ RasMol ]
		Asp B:22 - Pro B:23	[ RasMol ]
		Cys A:159 - Pro A:160	[ RasMol ]
		His A:30 - Pro A:31	[ RasMol ]
		Met B:183 - Pro B:184	[ RasMol ]
		Phe A:273 - Pro A:274	[ RasMol ]
		Ser A:278 - Pro A:279	[ RasMol ]
		Val B:140 - Pro B:141	[ RasMol ]

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	3ze9
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	Q72AS3_DESVH \| Q72AS3
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	Q72AS4_DESVH \| Q72AS4
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	1.12.7.2
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3ze6	3D STRUCTURE OF THE NI-FE-SE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE AS-ISOLATED OXIDIZED STATE AT 1.50 ANGSTROMS
3ze7	3D STRUCTURE OF THE NI-FE-SE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE REDUCED STATE AT 1.95 ANGSTROMS
3ze8	3D STRUCTURE OF THE NI-FE-SE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE REDUCED STATE AT 1.95 ANGSTROMS
3zea	3D STRUCTURE OF THE NIFESE HYDROGENASE FROM D. VULGARIS HILDENBOROUGH IN THE REDUCED STATE AT 1.82 ANGSTROMS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (9, 10)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 15)

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