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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MONOMERIC ACETYL-COA SYNTHASE FROM CARBOXYDOTHERMUS HYDROGENOFORMANS
 
Authors :  V. Svetlitchnyi, H. Dobbek, W. Meyer-Klaucke, T. Meins, B. Thiele, P. R R. Huber, O. Meyer
Date :  11 Dec 03  (Deposition) - 23 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Nickel, Cluster A, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Svetlitchnyi, H. Dobbek, W. Meyer-Klaucke, T. Meins, B. Thiele, P. Rmer, R. Huber, O. Meyer
A Functional Ni-Ni-[4Fe-4S] Cluster In The Monomeric Acetyl-Coa Synthase From Carboxydothermus Hydrogenoformans
Proc. Natl. Acad. Sci. Usa V. 101 446 2004
PubMed-ID: 14699043  |  Reference-DOI: 10.1073/PNAS.0304262101

(-) Compounds

Molecule 1 - ACETYL-COA SYNTHASE
    Chains: A
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 129958

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2NI2Ligand/IonNICKEL (II) ION
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:512 , CYS A:598 , CYS A:600 , SF4 A:733 , NI A:735 , HOH A:736BINDING SITE FOR RESIDUE NI A 734
02AC2SOFTWARECYS A:598 , GLY A:599 , CYS A:600 , PHE A:601 , NI A:734BINDING SITE FOR RESIDUE NI A 735
03AC3SOFTWARECYS A:509 , CYS A:512 , CYS A:521 , CYS A:531 , ILE A:534 , CYS A:598 , CYS A:600 , NI A:734BINDING SITE FOR RESIDUE SF4 A 733
04AC4SOFTWAREGLU A:40 , LEU A:43 , SER A:44 , ASN A:87BINDING SITE FOR RESIDUE GOL A 959
05AC5SOFTWARETYR A:38 , MET A:263 , VAL A:264BINDING SITE FOR RESIDUE GOL A 960
06AC6SOFTWARETYR A:38 , SER A:44 , GOL A:968BINDING SITE FOR RESIDUE GOL A 961
07AC7SOFTWAREVAL A:56 , GLY A:57 , TYR A:58 , THR A:61 , PHE A:64 , VAL A:76 , ARG A:77 , HOH A:851BINDING SITE FOR RESIDUE GOL A 962
08AC8SOFTWAREASN A:87 , ARG A:90 , ALA A:91 , HOH A:886BINDING SITE FOR RESIDUE GOL A 963
09AC9SOFTWAREALA A:502 , LYS A:540 , GOL A:965BINDING SITE FOR RESIDUE GOL A 964
10BC1SOFTWAREVAL A:503 , ASP A:504 , THR A:505 , TYR A:507 , GOL A:964BINDING SITE FOR RESIDUE GOL A 965
11BC2SOFTWARELEU A:608 , GLU A:610 , GOL A:967BINDING SITE FOR RESIDUE GOL A 966
12BC3SOFTWAREMET A:629 , MET A:637 , PHE A:647 , GOL A:966BINDING SITE FOR RESIDUE GOL A 967
13BC4SOFTWARESER A:44 , ARG A:45 , GLU A:48 , GOL A:961BINDING SITE FOR RESIDUE GOL A 968
14BC5SOFTWARETYR A:63 , LEU A:230 , HOH A:757 , HOH A:795BINDING SITE FOR RESIDUE GOL A 969
15BC6SOFTWAREILE A:156 , GLY A:183BINDING SITE FOR RESIDUE GOL A 970

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:598 -A:600

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:133 -Pro A:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RU3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RU3)

(-) Exons   (0, 0)

(no "Exon" information available for 1RU3)

(-) Sequences/Alignments

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:728
 aligned with P83789_CARHY | P83789 from UniProtKB/TrEMBL  Length:732

    Alignment length:728
                                    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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724        
         P83789_CARHY     5 INFDQIFEGAIEPGKEPKRLFKEVYEGAITATSYAEILLSRAIEKYGPDHPVGYPDTAYFLPVIRAFSGEEVRTLKDMVPILNRMRAQIKSELTFENARLAGEATWYAAEIIEALRYLKHTPENPIVVPPWTGFIGDPVVRQYGIKMVDWTIPGEAIIIGRAKDSKAAKKIVDDLMGKGLMLFLCDEIIEQLLEENVKLGVDYIAYPLGNFTQVVHAANYALRAGLMFGGIAPGLRDAHRDYQRRRVLAFVLYLGEHDMVKTAAAMGAIFTGFPVITDQPLPEDKQIKDWFISEPDYDKIVQTALEVRGIKITSIDIDLPINFGPAFEGESIRKGDMHVEFGGGKTPSFELVRMVGPDEIEDGKVEVIGPDIDSVEPGGRLPIGIVVDIYGRKMQEDFEPVLERRIHYFTNYGEGFWHTAQRDLTWVRISKEAFAKGARLKHLGQLLYAKFKQEFPSIVDRVQVTIYTDEQKVLELREIARKKYAERDARLRELSDEAVDTYYSCLLCQSFAPTHVCIVSPERVGLCGAISWLDAKAAYEINPNGPNQPIPKEGLIDPVKGQWESFNEYIYKNSQRTIERMNLYTIMEYPMTSCGCFEAIMAYLPELNGFMIVNREHSGMTPIGMTFSTLAGMVGGGTQTPGFMGIGKSYIGSRKFVKADGGLARVVWMPKDLKEQLRSIIEERAEEEGLGRDFIDKIADETVGTTVDEVLPFLEEKGHPALSMEPLL 732
               SCOP domains d1ru3a_ A: Monomeric acetyl-CoA synthase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1ru3A01 A:5-124 Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1                                          1ru3A02 A:125-314  [code=3.40.50.2030, no name defined]                                                                                                                                       ------1ru3A03 A:321-498 Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 3                                                                     1ru3A04 A:499-587 Carbon monoxide dehydrogenase alpha subunit. Chain D, domain 4         ---------------1ru3A05 A:603-732 Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase(codh/acs), Chain M, domain 5                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CdhC-1ru3A01 A:320-732                                                                                                                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author .hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhh.....hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh....hhhh.eeeee.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhh...eee.............eee.....hhhhhhhhhhh..............hhhhh........eeeeee.......eeeee........................ee....eeeeee....hhhhhhhhhhhhhhhhh....eeee......eeeeehhhhhh..hhhhhhhhhhhhhhhh......eeeee...hhhhhhhh...hhhhhhhhhhhhhhh......eeeeehhhhhh.....eee...........hhhhhhhhhhhh......eee...eee....eehhhhhhhhhhh........................eeeeee....eeeeee...........hhhhhhhhhh.......eeeehhhhhhh...hhhhhhhh.eee.hhhhhhhhhhhhhhhhhhh....hhhhhh.......hhhhhhhhhhhh.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ru3 A   5 INFDQIFEGAIEPGKEPKRLFKEVYEGAITATSYAEILLSRAIEKYGPDHPVGYPDTAYFLPVIRAFSGEEVRTLKDMVPILNRMRAQIKSELTFENARLAGEATWYAAEIIEALRYLKHTPENPIVVPPWTGFIGDPVVRQYGIKMVDWTIPGEAIIIGRAKDSKAAKKIVDDLMGKGLMLFLCDEIIEQLLEENVKLGVDYIAYPLGNFTQVVHAANYALRAGLMFGGIAPGLRDAHRDYQRRRVLAFVLYLGEHDMVKTAAAMGAIFTGFPVITDQPLPEDKQIKDWFISEPDYDKIVQTALEVRGIKITSIDIDLPINFGPAFEGESIRKGDMHVEFGGGKTPSFELVRMVGPDEIEDGKVEVIGPDIDSVEPGGRLPIGIVVDIYGRKMQEDFEPVLERRIHYFTNYGEGFWHTAQRDLTWVRISKEAFAKGARLKHLGQLLYAKFKQEFPSIVDRVQVTIYTDEQKVLELREIARKKYAERDARLRELSDEAVDTYYSCLLCQSFAPTHVCIVSPERVGLCGAISWLDAKAAYEINPNGPNQPIPKEGLIDPVKGQWESFNEYIYKNSQRTIERMNLYTIMEYPMTSCGCFEAIMAYLPELNGFMIVNREHSGMTPIGMTFSTLAGMVGGGTQTPGFMGIGKSYIGSRKFVKADGGLARVVWMPKDLKEQLRSIIEERAEEEGLGRDFIDKIADETVGTTVDEVLPFLEEKGHPALSMEPLL 732
                                    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       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (5, 5)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CdhC] (4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P83789_CARHY | P83789)
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: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:0006084    acetyl-CoA metabolic process    The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.
    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.

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