Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  COMPLETE STRUCTURE OF THE CORRINOID,IRON-SULFUR PROTEIN INCLUDING THE N-TERMINAL DOMAIN WITH A 4FE-4S CLUSTER
 
Authors :  S. Goetzl, J. H. Jeoung, S. E. Hennig, H. Dobbek
Date :  16 Mar 11  (Deposition) - 08 Jun 11  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Goetzl, J. H. Jeoung, S. E. Hennig, H. Dobbek
Structural Basis For Electron And Methyl-Group Transfer In A Methyltransferase System Operating In The Reductive Acetyl-Coa Pathway
J. Mol. Biol. V. 411 96 2011
PubMed-ID: 21640123  |  Reference-DOI: 10.1016/J.JMB.2011.05.025

(-) Compounds

Molecule 1 - CARBON MONOXIDE DEHYDROGENASE CORRINOID/IRON-SULFUR PROTEIN, GAMMA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 246194
    Strain: Z-2901
 
Molecule 2 - CO DEHYDROGENASE/ACETYL-COA SYNTHASE, IRON-SULFUR PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 246194
    Strain: Z-2901

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1B121Ligand/IonCOBALAMIN
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:337 , ILE A:338 , THR A:339 , PHE A:342 , THR A:345 , CYS A:348 , VAL A:349 , GLY A:369 , THR A:370 , SER A:371 , VAL A:372 , LEU A:373 , THR A:374 , ILE A:405 , PRO A:407 , PRO A:429 , ARG A:430 , SER A:432 , HOH A:2482 , HOH A:2496 , HOH A:2498 , HOH A:2499 , HOH A:2503 , HOH A:2505 , HOH A:2506 , PRO B:181 , LEU B:182 , LEU B:209 , ILE B:210 , GLY B:211 , TYR B:215 , GLU B:249 , HOH B:2176 , HOH B:2180 , HOH B:2210BINDING SITE FOR RESIDUE B12 A1442
2AC2SOFTWAREPRO A:13 , LYS A:15 , ASN A:16 , CYS A:17 , LYS A:18 , CYS A:20 , CYS A:25 , PHE A:28 , CYS A:42BINDING SITE FOR RESIDUE SF4 A1443

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:182 -Ala A:183
2Ser B:155 -Ser B:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YCL)

(-) 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:443
 aligned with Q3ACS3_CARHZ | Q3ACS3 from UniProtKB/TrEMBL  Length:445

    Alignment length:443
                                    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   
         Q3ACS3_CARHZ     2 GLTGLEIYKHLPKKNCKECGQPTCLAFAMQIAAGKAGLDACPYVSDEAKELLESASAPPVALIKVGKGEKVLEIGHETVLFRHDKRFEHPCGLAILVEDTLSEGEIKERVEKINKLVFDRVGQMHSVNLVALKGSSQDAATFAKAVATAREVTDLPFILIGTPEQLAAALETEGANNPLLYAATADNYEQMVELAKKYNVPLTVSAKGLDALAELVQKITALGYKNLILDPQPENISEGLFYQTQIRRLAIKKLFRPFGYPTIAFALDENPYQAVMEASVYIAKYAGIIVLNTVEPADILPLITLRLNIYTDPQKPIAVEPKVYEILNPGPDAPVFITTNFSLTYFCVAGDVEGARIPAYILPVDTDGTSVLTAWAAGKFTPEKIAQFLKESGIAEKVNHRKAILPGGVAVLSGKLQELSGWEILVGPRESSGINSFIKQRWN 444
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------FeS-2yclA01 A:11-45                -----------------CdhD-2yclA02 A:63-439                                                                                                                                                                                                                                                                                                                                                                    ----- Pfam domains
         Sec.struct. author ..hhhhhhh.............hhhhhhhhhhh...hhhhh...hhhhhhhhhh........eee.hhhhheee.................eeeeeee...hhhhhhhhhhhhhh.eeee..eeee..eeeee....hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhhh.hhhhh...eeee...hhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.............eee........eeeee.hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycl A   2 GLTGLEIYKHLPKKNCKECGQPTCLAFAMQIAAGKAGLDACPYVSDEAKELLESASAPPVALIKVGKGEKVLEIGHETVLFRHDKRFEHPCGLAILVEDTLSEGEIKERVEKINKLVFDRVGQMHSVNLVALKGSSQDAATFAKAVATAREVTDLPFILIGTPEQLAAALETEGANNPLLYAATADNYEQMVELAKKYNVPLTVSAKGLDALAELVQKITALGYKNLILDPQPENISEGLFYQTQIRRLAIKKLFRPFGYPTIAFALDENPYQAVMEASVYIAKYAGIIVLNTVEPADILPLITLRLNIYTDPQKPIAVEPKVYEILNPGPDAPVFITTNFSLTYFCVAGDVEGARIPAYILPVDTDGTSVLTAWAAGKFTPEKIAQFLKESGIAEKVNHRKAILPGGVAVLSGKLQELSGWEILVGPRESSGINSFIKQRWN 444
                                    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   


Chain B from PDB  Type:PROTEIN  Length:309
 aligned with Q3ACS0_CARHZ | Q3ACS0 from UniProtKB/TrEMBL  Length:310

    Alignment length:309
                                    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         
         Q3ACS0_CARHZ     2 AVEVLKEKWNSKVVEVTLGTGDKTVTLGGDSTLPFLTFEGEMPNPPRFALEVFDTPPTDWPDILVEPFKDVINDPVAWAKKCVEYGADIVALRLVSAHPDGQNRSGAELAEVCKAVADAIDVPLMIIGCGVEEKDAEIFPVIGEALSGRNCLLSSATKDNYKPIVATCMVHGHSVVASAPLDINLSKQLNIMIMEMNLAPNRIIMDPLIGALGYGIEYSYSIIERMRLGALTGDKILAMPVVCFIGQEAWKAKEAKDPEVAEWGDYALRAIHWETVTTVALIQAGGHLFVMRHPKSLAEVKEHLKRILK 310
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------CdhD-2yclB01 B:16-300                                                                                                                                                                                                                                                                        ---------- Pfam domains
         Sec.struct. author ..............eeee.hhhhheeee..................eeeeeee.......hhhhhhhhh....hhhhhhhhhhhh...eeeee.hhhh......hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhh...hhh.eeee........hhhhhhhhhhhhhhhhhh.hhhhh...eehhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ycl B   2 AVEVLKEKWNSKVVEVTLGTGDKTVTLGGDSTLPFLTFEGEMPNPPRFALEVFDTPPTDWPDILVEPFKDVINDPVAWAKKCVEYGADIVALRLVSAHPDGQNRSGAELAEVCKAVADAIDVPLMIIGCGVEEKDAEIFPVIGEALSGRNCLLSSATKDNYKPIVATCMVHGHSVVASAPLDINLSKQLNIMIMEMNLAPNRIIMDPLIGALGYGIEYSYSIIERMRLGALTGDKILAMPVVCFIGQEAWKAKEAKDPEVAEWGDYALRAIHWETVTTVALIQAGGHLFVMRHPKSLAEVKEHLKRILK 310
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 2YCL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: 4Fe-4S (51)
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (13, 19)

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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    B12  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser B:155 - Ser B:156   [ RasMol ]  
    Tyr A:182 - Ala A:183   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2ycl
    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
  Q3ACS0_CARHZ | Q3ACS0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q3ACS3_CARHZ | Q3ACS3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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

(-) Analysis Tools

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
  Q3ACS0_CARHZ | Q3ACS0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q3ACS3_CARHZ | Q3ACS3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q3ACS0_CARHZ | Q3ACS0: 2h9a 4c1n
        Q3ACS3_CARHZ | Q3ACS3: 2h9a 4c1n

(-) Related Entries Specified in the PDB File

2yci METHYLTRANSFERASE NATIVE
2ycj METHYLTRANSFERASE BOUND WITH METHYLTETRAHYDROFOLATE
2yck METHYLTRANSFERASE BOUND WITH TETRAHYDROFOLATE