2YIV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   NI,FE-CODH WITH N-BUTYLISOCYANATE STATE

Authors :   J. H. Jeoung, H. Dobbek

Date :   16 May 11 (Deposition) - 28 Mar 12 (Release) - 14 Nov 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.28

Chains :   Asym. Unit : X
Biol. Unit 1: X  (2x)

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. H. Jeoung, H. Dobbek
N-Butyl Isocyanide Oxidation At The [Nife4S4Oh(X)] Cluster Of Co Dehydrogenase.
J. Biol. Inorg. Chem. V. 17 167 2012
PubMed-ID: 21904889 | Reference-DOI: 10.1007/S00775-011-0839-Y

Molecule 1 - CARBON MONOXIDE DEHYDROGENASE 2
	Chains	:	X
	EC Number	:	1.2.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA
	Expression System Vector	:	PET28
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	CARBOXYDOTHERMUS HYDROGENOFORMANS
	Organism Taxid	:	129958
	Strain	:	Z-2091
	Synonym	:	CODH 2

		1
Asymmetric Unit	:	X
Biological Unit 1 (2x)	:	X

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 6)

No.	Name	Count	Type	Full Name
1	FE	1	Ligand/Ion	FE (III) ION
2	FES	1	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NBN	1	Ligand/Ion	N-BUTYL ISOCYANIDE
4	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
5	WCC	1	Ligand/Ion	FE(3)-NI(1)-S(4) CLUSTER
6	YIV	1	Ligand/Ion	N-BUTYLFORMAMIDE

Biological Unit 1 (5, 10)

No.	Name	Count	Type	Full Name
1	FE	-1	Ligand/Ion	FE (III) ION
2	FES	2	Ligand/Ion	FE2/S2 (INORGANIC) CLUSTER
3	NBN	2	Ligand/Ion	N-BUTYL ISOCYANIDE
4	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER
5	WCC	2	Ligand/Ion	FE(3)-NI(1)-S(4) CLUSTER
6	YIV	2	Ligand/Ion	N-BUTYLFORMAMIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS X:48 , CYS X:51 , GLY X:54 , CYS X:56 , CYS X:70 , ARG X:80 , MET X:199	BINDING SITE FOR RESIDUE SF4 X5000
2	AC2	SOFTWARE	CYS X:39 , GLY X:42 , CYS X:47	BINDING SITE FOR RESIDUE FES X5001
3	AC3	SOFTWARE	HIS X:261 , CYS X:294 , CYS X:295 , SER X:312 , CYS X:333 , GLY X:445 , CYS X:446 , CYS X:476 , CYS X:526 , MET X:560 , LYS X:563 , YIV X:5003 , FE X:5004 , HOH X:5100	BINDING SITE FOR RESIDUE WCC X5002
4	AC4	SOFTWARE	HIS X:93 , ALA X:444 , GLY X:445 , CYS X:526 , LYS X:563 , ALA X:564 , ILE X:567 , WCC X:5002 , HOH X:5100	BINDING SITE FOR RESIDUE YIV X5003
5	AC5	SOFTWARE	HIS X:261 , CYS X:295 , CYS X:526 , LYS X:563 , WCC X:5002 , HOH X:5100	BINDING SITE FOR RESIDUE FE X5004
6	AC6	SOFTWARE	LEU X:82 , VAL X:565 , ILE X:580 , PRO X:584 , ILE X:586 , PHE X:608	BINDING SITE FOR RESIDUE NBN X5005

(no "SS Bond" information available for 2YIV)

Asymmetric Unit

No.	Residues
1	Lys X:36	-	Pro X:37
2	Gly X:54	-	Pro X:55
3	Glu X:64	-	Pro X:65

(no "SAP(SNP)/Variant" information available for 2YIV)

(no "PROSITE Motif" information available for 2YIV)

(no "Exon" information available for 2YIV)

Asymmetric 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 X from PDB  Type:PROTEIN  Length:635
 aligned with COOS2_CARHZ | Q9F8A8 from UniProtKB/Swiss-Prot  Length:636

    Alignment length:635
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631     
          COOS2_CARHZ     2 AKQNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGDEPKVGICGATAEVIVARGLDRSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKLHSIAKRLGIPTEGQKDEDIALEVAKAALADFHEKDTPVLWVTTVLPPSRVKVLSAHGLIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPVVTESNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGATGINVVGICCTGNEVLMRHGIPACTHSVSQEMAMITGALDAMILDYQCIQPSVATIAECTGTTVITTMEMSKITGATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKVVAGFSTEAIINALSKLNANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAGALMRHGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRAVALVAALANRLGVDLDRLPVVASAAEAMHEKAVAIGTWAVTIGLPTHIGVLPPITGSLPVTQILTSSVKDITGGYFIVELDPETAADKLLAAINERRAGLGLPW 636
               SCOP domains d2yivx_ X: Ni-containing carbon monoxide dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhh.ee.......ee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.......hhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh..eeehhhhhhhhhhh..eeeeee.......hhhhhhhhhh.eeee..........ee...hhhhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhh.....hhhhhhhhhhh.....eeee..........hhhhhhhhhhhhhh..eeeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhhhh.hhhhh.eeeee....hhhhhhhhhhhhhh..eeee........hhhhhhhhhh.hhhhhh.eeee..hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yiv X   2 ARQNLKSTDRAVQQMLDKAKREGIQTVWDRYEAMKPQCGFGETGLCCRHCLQGPCRINPFGDEPKVGICGATAEVIVARGLDRSIAAGAAGHSGHAKHLAHTLKKAVQGKAASYMIKDRTKLHSIAKRLGIPTEGQKDEDIALEVAKAALADFHEKDTPVLWVTTVLPPSRVKVLSAHGLIPAGIDHEIAEIMHRTSMGCDADAQNLLLGGLRCSLADLAGCYMGTDLADILFGTPAPVVTESNLGVLKADAVNVAVHGHNPVLSDIIVSVSKEMENEARAAGATGINVVGICCTGNEVLMRHGIPACTHSVSQEMAMITGALDAMILDYQCIQPSVATIAECTGTTVITTMEMSKITGATHVNFAEEAAVENAKQILRLAIDTFKRRKGKPVEIPNIKTKVVAGFSTEAIINALSKLNANDPLKPLIDNVVNGNIRGVCLFAGCNNVKVPQDQNFTTIARKLLKQNVLVVATGCGAGALMRHGFMDPANVDELCGDGLKAVLTAIGEANGLGGPLPPVLHMGSCVDNSRAVALVAALANRLGVDLDRLPVVASAAEAMHEKAVAIGTWAVTIGLPTHIGVLPPITGSLPVTQILTSSVKDITGGYFIVELDPETAADKLLAAINERRAGLGLPW 636
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631

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 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: Carbon monoxide dehydrogenase (15)

Protein domain: Ni-containing carbon monoxide dehydrogenase (10)

Carboxydothermus hydrogenoformans [TaxId: 129958] (9)

d2yivx_

(no "CATH Domain" information available for 2YIV)

(no "Pfam Domain" information available for 2YIV)

Asymmetric Unit(hide GO term definitions)

Chain X (COOS2_CARHZ | Q9F8A8)

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:0018492	carbon-monoxide dehydrogenase (acceptor) activity	Catalysis of the reaction: CO + H2O + acceptor = CO2 + reduced acceptor.
	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: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:0019415	acetate biosynthetic process from carbon monoxide	The chemical reactions and pathways resulting in the formation of acetate from other compounds, including carbon monoxide.
	GO:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		FE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FES	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NBN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SF4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		WCC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		YIV	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu X:64 - Pro X:65	[ RasMol ]
		Gly X:54 - Pro X:55	[ RasMol ]
		Lys X:36 - Pro X:37	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2yiv
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	COOS2_CARHZ \| Q9F8A8
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.2.99.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	COOS2_CARHZ \| Q9F8A8
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	COOS2_CARHZ \| Q9F8A8	:	1su6 1su7 1su8 1suf 3b51 3b52 3b53 3i39 4udx 4udy 5fle

1su6	CARBON MONOXIDE DEHYDROGENASE FROM CARBOXYDOTHERMUSHYDROGENOFORMANS: CO REDUCED STATE
1su7	CARBON MONOXIDE DEHYDROGENASE FROM CARBOXYDOTHERMUSHYDROGENOFORMANS- DTT REDUCED STATE
1su8	CARBON MONOXIDE INDUCED DECOMPOSITION OF THE ACTIVE SITE [NI-4FE-5S] CLUSTER OF CO DEHYDROGENASE
1suf	CARBON MONOXIDE DEHYDROGENASE FROM CARBOXYDOTHERMUSHYDROGENOFORMANS-INACTIVE STATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File