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(-) Description

Title :  ISOBUTYRYL-COA MUTASE FUSED WITH BOUND BUTYRYL-COA, GDP, AND MG AND WITHOUT COBALAMIN (APO-ICMF/GDP)
 
Authors :  M. Jost, C. L. Drennan
Date :  17 Dec 14  (Deposition) - 11 Feb 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Radical Enzyme, Complex, Isomerase, G-Protein Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jost, V. Cracan, P. A. Hubbard, R. Banerjee, C. L. Drennan
Visualization Of A Radical B12 Enzyme With Its G-Protein Chaperone.
Proc. Natl. Acad. Sci. Usa V. 112 2419 2015
PubMed-ID: 25675500  |  Reference-DOI: 10.1073/PNAS.1419582112

(-) Compounds

Molecule 1 - ISOBUTYRYL-COA MUTASE FUSED
    Chains: A, B
    EC Number: 5.4.99.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ICMF, RMET_0210
    Organism Scientific: RALSTONIA METALLIDURANS (STRAIN CH34 / ATCC 43123 / DSM 2839)
    Organism Taxid: 266264
    Other Details: ICMF IS MISANNOTATED AS SBM IN THE GENOME OF CUPRIAVIDUS METALLIDURANS.
    Strain: CH34 / ATCC 43123 / DSM 2839

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1BCO2Ligand/IonBUTYRYL COENZYME A
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:585 , PHE A:587 , ARG A:589 , ARG A:596 , PHE A:598 , ARG A:622 , SER A:677 , THR A:679 , ARG A:728 , THR A:730 , GLN A:732 , TYR A:772 , HIS A:780 , SER A:821 , PHE A:823 , ARG A:856 , LYS A:861 , TYR A:862 , HIS A:863 , GLN A:865 , SER A:897binding site for residue BCO A 1101
2AC2SOFTWAREGLY A:219 , ALA A:220 , GLY A:221 , LYS A:222 , SER A:223 , SER A:224 , ASP A:262 , ARG A:265 , GLU A:310 , ASN A:357 , LYS A:358 , ASP A:360 , GLN A:395 , ALA A:396 , SER A:397 , GLU A:973 , ASN A:1092 , MG A:1103binding site for residue GDP A 1102
3AC3SOFTWARESER A:223 , ASP A:262 , GLU A:310 , GDP A:1102binding site for residue MG A 1103
4AC4SOFTWAREILE A:248 , ASP A:249 , ASP A:262 , GLU A:310 , THR A:311binding site for residue MG A 1104
5AC5SOFTWAREPHE B:585 , PHE B:587 , TYR B:772 , SER B:821 , ASN B:896 , SER B:897binding site for residue BCO B 1101
6AC6SOFTWAREGLY B:219 , ALA B:220 , GLY B:221 , LYS B:222 , SER B:223 , SER B:224 , ARG B:265 , GLU B:310 , ALA B:338 , GLN B:341 , ASN B:357 , LYS B:358 , ASP B:360 , GLN B:395 , ALA B:396 , SER B:397 , GLU B:973 , ASN B:1092 , MG B:1103binding site for residue GDP B 1102
7AC7SOFTWARESER B:223 , GLY B:261 , ASP B:262 , GLU B:310 , LYS B:344 , GDP B:1102binding site for residue MG B 1103
8AC8SOFTWAREILE B:248 , ASP B:249 , ASP B:262 , GLU B:310 , THR B:311binding site for residue MG B 1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XC8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:578 -Pro A:579
2Phe B:578 -Pro B:579

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XC8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XC8)

(-) Exons   (0, 0)

(no "Exon" information available for 4XC8)

(-) 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:1058
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..........hhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eeee......hhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee........ee..hhhhh.......eeeeeee..........hhhhhhhhhhhh...eeeeeeee.......hhhhh.eeeeee.....hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....hhhhh.eee.......hhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eee.....eee........hhhhhhhhhhhh........................eee...hhhhhhhhhhhhh.....eeeeee.hhhhhh......hhhhhh..........hhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eee..hhhhhh........hhhhhhhhhhhhhhhhhhh....ee.eeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc8 A   22 GPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVVTAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIVPDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLDTVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGAGKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAINHPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAAIVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDVAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMSLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQAYSGDEYVEIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGSFPYTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVSMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDPRSSEDEKQSQLHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1093
                                    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       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007    ||1025      1035      1045      1055      1065      1075      1085        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     529|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        1012|                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      536                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         1021                                                                        


Chain B from PDB  Type:PROTEIN  Length:1060
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee......hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee........ee..hhhhh.......eeeeeee..........hhhhhhhhhhhh...eeeeeeee.......hhhhh.eeeeee.....hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh.....hhhhh.eee.......hhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eee.....eee........hhhhhhhhhhhh........................eee...hhhhhhhhhhhhh.....eeeeee.hhhhhh......hhhhhh..........hhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.eee..hhhhhhhh......hhhhhhhhhhhhhhhhhhh....ee.eeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..eeeeee...hhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeee.........hhhhhhhhhhhhhhhhhhh...eee.............hhhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc8 B   22 GPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVVTAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIVPDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLDTVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGAGKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAINHPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAAIVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDVAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMSLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQAYSGDEYVVIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGSFPYTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVSMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDPLARSSEDEKQSQLHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1093
                                    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       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007    ||1023      1033      1043      1053      1063      1073      1083      1093
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      530|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       1012|                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       537                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        1019
   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 4XC8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XC8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XC8)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xc8
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  ICMF_CUPMC | Q1LRY0
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  5.4.99.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        ICMF_CUPMC | Q1LRY0: 4xc6 4xc7 5cjt 5cju 5cjv 5cjw

(-) Related Entries Specified in the PDB File

4xc6 SAME PROTEIN BOUND TO ADENOSYLCOBALAMIN AND GDP.
4xc7 SAME PROTEIN WITHOUT BOUND COFACTORS, BUT WITH BOUND BUTYRYL-COA.