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(-) Description

Title :  CO-DEPENDENT TRANSCRIPTION FACTOR COOA FROM CARBOXYDOTHERMUS HYDROGENOFORMANS (IMIDAZOLE-BOUND FORM)
 
Authors :  Y. Higuchi, H. Komori
Date :  10 Jan 06  (Deposition) - 16 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dna Transcription Regulator, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Komori, S. Inagaki, S. Yoshioka, S. Aono, Y. Higuchi
Crystal Structure Of Co-Sensing Transcription Activator Coo Bound To Exogenous Ligand Imidazole
J. Mol. Biol. V. 367 864 2007
PubMed-ID: 17292914  |  Reference-DOI: 10.1016/J.JMB.2007.01.043

(-) Compounds

Molecule 1 - CARBON MONOXIDE OXIDATION SYSTEM TRANSCRIPTION REGULATOR COOA-1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET28
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: CARBOXYDOTHERMUS HYDROGENOFORMANS
    Organism Taxid: 129958
    Synonym: COOA

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD4Ligand/IonIMIDAZOLE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:78 , PHE A:79 , CYS A:80 , HIS A:82 , THR A:83 , ARG A:84 , ILE A:100 , GLN A:104 , MET A:117 , IMD A:301 , GLN B:1004 , LEU B:1007 , LEU B:1125 , LYS B:1126 , LEU B:1129 , LYS B:1194BINDING SITE FOR RESIDUE HEM A 300
2AC2SOFTWAREGLN A:4 , MET A:5 , LEU A:125 , LYS A:126 , ILE B:1078 , PHE B:1079 , CYS B:1080 , HIS B:1082 , THR B:1083 , ARG B:1084 , ILE B:1100 , GLN B:1104 , VAL B:1107 , MET B:1117 , IMD B:1301 , HOH B:4088BINDING SITE FOR RESIDUE HEM B 1300
3AC3SOFTWAREILE C:2078 , PHE C:2079 , CYS C:2080 , HIS C:2082 , THR C:2083 , ARG C:2084 , ILE C:2100 , GLN C:2104 , MET C:2117 , IMD C:2301 , HOH C:4067 , GLN D:3004 , MET D:3005 , LEU D:3007 , LEU D:3125 , LYS D:3126 , LEU D:3129BINDING SITE FOR RESIDUE HEM C 2300
4AC4SOFTWAREGLN C:2004 , MET C:2005 , LEU C:2007 , LEU C:2125 , LYS C:2126 , LEU C:2129 , HOH C:4197 , ILE D:3078 , PHE D:3079 , CYS D:3080 , HIS D:3082 , THR D:3083 , ARG D:3084 , ILE D:3100 , PHE D:3103 , VAL D:3107 , MET D:3117 , IMD D:3301BINDING SITE FOR RESIDUE HEM D 3300
5AC5SOFTWAREHEM A:300 , MET B:1005 , VAL B:1118BINDING SITE FOR RESIDUE IMD A 301
6AC6SOFTWAREMET A:5 , VAL A:118 , HEM B:1300BINDING SITE FOR RESIDUE IMD B 1301
7AC7SOFTWAREHEM C:2300 , MET D:3005 , VAL D:3118BINDING SITE FOR RESIDUE IMD C 2301
8AC8SOFTWAREMET C:2005 , VAL C:2118 , HEM D:3300BINDING SITE FOR RESIDUE IMD D 3301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FMY)

(-) Sequences/Alignments

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 A from PDB  Type:PROTEIN  Length:218
 aligned with Q3AB29_CARHZ | Q3AB29 from UniProtKB/TrEMBL  Length:217

    Alignment length:218
                               1                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
        Q3AB29_CARHZ      - ---MRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS  215
               SCOP domains d2fmya1 A:2-138 automated matches                                                                                                        d2fmya2 A:139-219 automated matches                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.hhhhheeeee....eee.......eeeeeee.eeeeeee....eeeeeeee...eee.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee....eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fmy A    2 ATQMRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS  219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q3AB29_CARHZ | Q3AB29 from UniProtKB/TrEMBL  Length:217

    Alignment length:218
                               1                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
        Q3AB29_CARHZ      - ---MRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS  215
               SCOP domains d2fmyb1 B:1002-1138 automated matches                                                                                                    d2fmyb2 B:1139-1219 automated matches                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.hhhhheeeee....eee.......eeeeeee..eeeeee....eeeeeee....eee.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fmy B 1002 ATQMRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS 1219
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211        


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with Q3AB29_CARHZ | Q3AB29 from UniProtKB/TrEMBL  Length:217

    Alignment length:218
                               1                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
        Q3AB29_CARHZ      - ---MRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS  215
               SCOP domains d2fmyc1 C:2002-2138 automated matches                                                                                                    d2fmyc2 C:2139-2219 automated matches                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhh.hhhhheeeee....eee.......eeeeeee..eeeeee....eeeeeee....eee.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..eeeee...hhhhhhhhh..hhhhhhhhhhhhhhh..eee....eeee.hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fmy C 2002 ATQMRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS 2219
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211        


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with Q3AB29_CARHZ | Q3AB29 from UniProtKB/TrEMBL  Length:217

    Alignment length:218
                               1                                                                                                                                                                                                                      
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207        
        Q3AB29_CARHZ      - ---MRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS  215
               SCOP domains d2fmyd1 D:3002-3138 automated matches                                                                                                    d2fmyd2 D:3139-3219 automated matches                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh...hhhhhh..eeeee....eee.......eeeeeee..eeeeee....eeeeeee....eee.....eeee...eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee..eeeee...hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee..eeee.hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fmy D 3002 ATQMRLTDTNLLEVLNSEEYSGVLKEFREQRYSKKAILYTPNTERNLVFLVKSGRVRVYLAYEDKEFTLAILEAGDIFCTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILERVNQRTLLLKDLQKLKEFSS 3219
                                  3011      3021      3031      3041      3051      3061      3071      3081      3091      3101      3111      3121      3131      3141      3151      3161      3171      3181      3191      3201      3211
   Legend:   → Mismatch (orange background)
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    → 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  (2, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q3AB29_CARHZ | Q3AB29)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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        Q3AB29_CARHZ | Q3AB29: 2hkx

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