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Asym./Biol. Unit (Jmol Viewer)

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Title :   AS-ISOLATED HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS X-RAY STRUCTURE AT 1.35A RESOLUTION USING IRON ANOMALOUS SIGNAL

Authors :   D. Aragao, S. Macedo, E. P. Mitchell, D. Coelho, C. V. Romao, M. Teixeira, P. F. Lindley

Date :   14 Oct 04 (Deposition) - 04 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A

Keywords :   Hybrid Cluster Protein, Anaerobic, Oxidised, As-Isolated, Desulfovibrio Vulgaris, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Aragao, E. P. Mitchell, C. F. Frazao, M. A. Carrondo, P. F. Lindley
Structural And Functional Relationships In The Hybrid Cluster Protein Family:Structure Of The Anaerobically Purified Hybrid Cluster Protein From Desulfovibrio Vulgaris At 1. 35 A Resolution
Acta Crystallogr. , Sect. D V. 64 665 2008
PubMed-ID: 18560155 | Reference-DOI: 10.1107/S0907444908009165
(for further references see the PDB file header)

Molecule 1 - HYDROXYLAMINE REDUCTASE
	Chains	:	A
	EC Number	:	1.7.-.-
	Engineered	:	YES
	Expression System	:	DESULFOVIBRIO VULGARIS
	Expression System Plasmid	:	PJSP104
	Expression System Strain	:	HILDENBOROUGH NCIMB8303
	Expression System Taxid	:	881
	Organism Scientific	:	DESULFOVIBRIO VULGARIS
	Organism Taxid	:	881
	Other Details	:	CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS406
	Strain	:	HILDENBOROUGH NCIMB8303
	Synonym	:	HYBRID CLUSTER PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CSS	1	Mod. Amino Acid	S-MERCAPTOCYSTEINE
2	FS2	1	Ligand/Ion	FE-S-O HYBRID CLUSTER
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:3 , PHE A:4 , GLN A:5 , CYS A:6 , THR A:9 , CYS A:15 , GLY A:19 , MET A:20 , CYS A:21 , LYS A:23 , THR A:71	BINDING SITE FOR RESIDUE SF4 A1554
2	AC2	SOFTWARE	HIS A:244 , GLU A:268 , ASN A:311 , CYS A:312 , CSS A:406 , CYS A:434 , CYS A:459 , GLU A:494 , LYS A:496	BINDING SITE FOR RESIDUE FS2 A1555

(no "SS Bond" information available for 1W9M)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:311	-	Cys A:312
2	Gly A:515	-	Pro A:516

(no "SAP(SNP)/Variant" information available for 1W9M)

(no "PROSITE Motif" information available for 1W9M)

(no "Exon" information available for 1W9M)

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:553
 aligned with HCP_DESVH | P31101 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:553
                                    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   
            HCP_DESVH     1 MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGCDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK 553
               SCOP domains d1w9ma_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1w9mA01 A:1-139  [code=1.20.1270.20, no name defined]                                                                                      1w9mA02 A:140-223  [code=1.20.1270.20, no name defined]                             -1w9mA03 A:225-375  [code=3.40.50.2030, no name defined]                                                                                                --1w9mA04 A:378-550  [code=3.40.50.2030, no name defined]                                                                                                                      --- CATH domains
               Pfam domains Prismane-1w9mA01 A:1-550                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              --- Pfam domains
         Sec.struct. author ........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhh...hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeee..hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhh..eee............hhhh.eeee........eee..........hhhhhhhhh...........eeee..hhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh...eeeee.hhhhhhh......ee..ee.eee..hhhhhhhhhhhhhhhhhhh...hhhhh.eeeeee..hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.ee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w9m A   1 MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGcDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK 553
                                    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   
                                                                                                                                                                                                                                                                                                                                                                                                                                               406-CSS

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Prismane protein-like (31)

Superfamily: Prismane protein-like (31)

Family: Hybrid cluster protein (prismane protein) (10)

Protein domain: automated matches (1)

Desulfovibrio vulgaris [TaxId: 881] (1)

d1w9ma_

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Prismane] (9)

Family: Prismane (9)

Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303) (2)

Prismane-1w9mA01

A:1-550

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HCP_DESVH | P31101)

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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0050418	hydroxylamine reductase activity	Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
	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.
	GO:0016661	oxidoreductase activity, acting on other nitrogenous compounds as donors	Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CSS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FS2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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	Cis Peptide Bonds
		Asn A:311 - Cys A:312	[ RasMol ]
		Gly A:515 - Pro A:516	[ RasMol ]

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	1w9m
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	HCP_DESVH \| P31101
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	1.7.-.-
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	HCP_DESVH \| P31101
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UniProtKB/Swiss-Prot
	HCP_DESVH \| P31101	:	1e1d 1e2u 1e9v 1gnt 1oa1

1e1d	HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS
1e2u	LOW TEMPERATURE STUCTURE OF HYBRID CLUSTER PROTEIN FROMDESULFOVIBRIO VULGARIS TO 1.6A
1e9v	XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS
1gnt	HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS. X-RAY STRUCTURE AT 1.25A RESOLUTION USING SYNCHROTRON RADIATION.
1oa1	REDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH STRUCTURE AT 1.55A RESOLUTION USING SYNCHROTRON RADIATION.

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (2, 4)

Pfam Domains (1, 1)

Gene Ontology (9, 9)

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