2H9A - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CORRINOID IRON-SULFUR PROTEIN

Authors :   H. Dobbek

Date :   09 Jun 06 (Deposition) - 26 Sep 06 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Heterodimer, Beta-Alpha-Barrels, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Svetlitchnaia, V. Svetlitchnyi, O. Meyer, H. Dobbek
Structural Insights Into Methyltransfer Reactions Of A Corrinoid Iron-Sulfur Protein Involved In Acetyl-Coa Synthesis.
Proc. Natl. Acad. Sci. Usa V. 103 14331 2006
PubMed-ID: 16983091 | Reference-DOI: 10.1073/PNAS.0601420103

Molecule 1 - CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
	Chains	:	A
	Organism Scientific	:	CARBOXYDOTHERMUS HYDROGENOFORMANS
	Organism Taxid	:	129958

Molecule 2 - CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
	Chains	:	B
	Organism Scientific	:	CARBOXYDOTHERMUS HYDROGENOFORMANS
	Organism Taxid	:	129958

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 18)

No.	Name	Count	Type	Full Name
1	B12	1	Ligand/Ion	COBALAMIN
2	IOD	16	Ligand/Ion	IODIDE ION
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN B:11	BINDING SITE FOR RESIDUE IOD B 1444
02	AC2	SOFTWARE	LYS A:253	BINDING SITE FOR RESIDUE IOD A 1445
03	AC3	SOFTWARE	ASN B:185 , HOH B:1597	BINDING SITE FOR RESIDUE IOD B 1446
04	AC4	SOFTWARE	LYS B:159 , GLN B:189	BINDING SITE FOR RESIDUE IOD B 1447
05	AC5	SOFTWARE	THR A:221	BINDING SITE FOR RESIDUE IOD A 1448
06	AC6	SOFTWARE	ASP A:120 , GLU B:263	BINDING SITE FOR RESIDUE IOD A 1450
07	AC7	SOFTWARE	HOH A:1555 , HOH A:1701	BINDING SITE FOR RESIDUE IOD A 1452
08	AC8	SOFTWARE	TRP A:376	BINDING SITE FOR RESIDUE IOD A 1453
09	AC9	SOFTWARE	LYS A:134 , HOH A:1550	BINDING SITE FOR RESIDUE IOD A 1455
10	BC1	SOFTWARE	SER A:127 , ASN A:129 , ARG A:307	BINDING SITE FOR RESIDUE IOD A 1456
11	BC2	SOFTWARE	SER A:433 , LYS B:254 , HOH B:1551	BINDING SITE FOR RESIDUE IOD B 1458
12	BC3	SOFTWARE	ASP B:122	BINDING SITE FOR RESIDUE IOD B 1459
13	BC4	SOFTWARE	PRO A:317 , PHE A:337 , ILE A:338 , THR A:339 , PHE A:342 , THR A:345 , VAL A:349 , GLY A:369 , THR A:370 , SER A:371 , VAL A:372 , THR A:374 , ALA A:377 , ILE A:405 , PRO A:407 , PRO A:429 , ARG A:430 , GLU A:431 , SER A:432 , HOH A:1460 , HOH A:1483 , HOH A:1493 , HOH A:1496 , HOH A:1502 , HOH A:1607 , HOH A:1627 , HOH A:1651 , HOH A:1679 , HOH A:1723 , HOH A:1730 , PRO B:181 , LEU B:182 , LEU B:186 , LEU B:209 , ILE B:210 , GLY B:211 , TYR B:215 , TYR B:219 , GLU B:249 , HOH B:1600	BINDING SITE FOR RESIDUE B12 A 1442

(no "SS Bond" information available for 2H9A)

(no "Cis Peptide Bond" information available for 2H9A)

(no "SAP(SNP)/Variant" information available for 2H9A)

(no "PROSITE Motif" information available for 2H9A)

(no "Exon" information available for 2H9A)

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:383
 aligned with Q3ACS3_CARHZ | Q3ACS3 from UniProtKB/TrEMBL  Length:445

    Alignment length:383
                                    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   
         Q3ACS3_CARHZ    59 PPVALIKVGKGEKVLEIGHETVLFRHDKRFEHPCGLAILVEDTLSEGEIKERVEKINKLVFDRVGQMHSVNLVALKGSSQDAATFAKAVATAREVTDLPFILIGTPEQLAAALETEGANNPLLYAATADNYEQMVELAKKYNVPLTVSAKGLDALAELVQKITALGYKNLILDPQPENISEGLFYQTQIRRLAIKKLFRPFGYPTIAFALDENPYQAVMEASVYIAKYAGIIVLNTVEPADILPLITLRLNIYTDPQKPIAVEPKVYEILNPGPDAPVFITTNFSLTYFCVAGDVEGARIPAYILPVDTDGTSVLTAWAAGKFTPEKIAQFLKESGIAEKVNHRKAILPGGVAVLSGKLQELSGWEILVGPRESSGINSFIKQ 441
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eee......hhhhh......eeeeeee...hhhhhhhhhhhhhh.eeee..eeee..eeeee....hhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhh.hhhhh...eee....hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.............eee........eeeee.hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h9a A  59 PPVALIKVGKGEKVLEIGHETVLFRHDKRFEHPCGLAILVEDTLSEGEIKERVEKINKLVFDRVGQMHSVNLVALKGSSQDAATFAKAVATAREVTDLPFILIGTPEQLAAALETEGANNPLLYAATADNYEQMVELAKKYNVPLTVSAKGLDALAELVQKITALGYKNLILDPQPENISEGLFYQTQIRRLAIKKLFRPFGYPTIAFALDENPYQAVMEASVYIAKYAGIIVLNTVEPADILPLITLRLNIYTDPQKPIAVEPKVYEILNPGPDAPVFITTNFSLTYFCVAGDVEGARIPAYILPVDTDGTSVLTAWAAGKFTPEKIAQFLKESGIAEKVNHRKAILPGGVAVLSGKLQELSGWEILVGPRESSGINSFIKQ 441
                                    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

Chain B from PDB  Type:PROTEIN  Length:307
 aligned with Q3ACS0_CARHZ | Q3ACS0 from UniProtKB/TrEMBL  Length:310

    Alignment length:307
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       
         Q3ACS0_CARHZ     3 VEVLKEKWNSKVVEVTLGTGDKTVTLGGDSTLPFLTFEGEMPNPPRFALEVFDTPPTDWPDILVEPFKDVINDPVAWAKKCVEYGADIVALRLVSAHPDGQNRSGAELAEVCKAVADAIDVPLMIIGCGVEEKDAEIFPVIGEALSGRNCLLSSATKDNYKPIVATCMVHGHSVVASAPLDINLSKQLNIMIMEMNLAPNRIIMDPLIGALGYGIEYSYSIIERMRLGALTGDKILAMPVVCFIGQEAWKAKEAKDPEVAEWGDYALRAIHWETVTTVALIQAGGHLFVMRHPKSLAEVKEHLKRIL 309
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee.hhhhheeee..................eeeeeee.......hhhhhhhhh....hhhhhhhhhhhh...eeeee.hhhh......hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh...hhh.eeee........hhhhhhhhhhhhhhhhhh.hhhhh...eehhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h9a B   3 VEVLKEKWNSKVVEVTLGTGDKTVTLGGDSTLPFLTFEGEMPNPPRFALEVFDTPPTDWPDILVEPFKDVINDPVAWAKKCVEYGADIVALRLVSAHPDGQNRSGAELAEVCKAVADAIDVPLMIIGCGVEEKDAEIFPVIGEALSGRNCLLSSATKDNYKPIVATCMVHGHSVVASAPLDINLSKQLNIMIMEMNLAPNRIIMDPLIGALGYGIEYSYSIIERMRLGALTGDKILAMPVVCFIGQEAWKAKEAKDPEVAEWGDYALRAIHWETVTTVALIQAGGHLFVMRHPKSLAEVKEHLKRIL 309
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302

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 "SCOP Domain" information available for 2H9A)

(no "CATH Domain" information available for 2H9A)

(no "Pfam Domain" information available for 2H9A)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q3ACS3_CARHZ | Q3ACS3)

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: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:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
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:0046356	acetyl-CoA catabolic process	The chemical reactions and pathways resulting in the breakdown of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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.

Chain B (Q3ACS0_CARHZ | Q3ACS0)

molecular function
	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:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
biological process
	GO:0006085	acetyl-CoA biosynthetic process	The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
	GO:0044237	cellular metabolic process	The chemical reactions and pathways by which individual cells transform chemical substances.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	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
(no "Cis Peptide Bonds" information available for 2h9a)

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	2h9a
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(no "Related Entries Specified in the PDB File" available for 2H9A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Gene Ontology (13, 19)

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