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(-) Description

Title :  ISOBUTYRYL-COA MUTASE FUSED WITH BOUND ADENOSYLCOBALAMIN, GDP, AND MG (HOLO-ICMF/GDP)
 
Authors :  M. Jost, C. L. Drennan
Date :  17 Dec 14  (Deposition) - 11 Feb 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
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  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
15AD1Ligand/Ion5'-DEOXYADENOSINE
2ACT1Ligand/IonACETATE ION
3B122Ligand/IonCOBALAMIN
4GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
5MG4Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:36 , ASP A:37 , GLY A:38 , HIS A:39 , ASP A:40 , ALA A:41 , SER A:42 , MET A:46 , TYR A:86 , GLN A:87 , GLY A:88 , GLY A:114 , GLY A:116 , VAL A:118 , TYR A:136 , SER A:137 , PRO A:138 , ALA A:626 , PHE A:627 , LEU A:632 , SER A:650 , GLY A:741 , GLN A:742 , THR A:744 , GLU A:783 , ALA A:784 , GLY A:868 , ARG A:869 , LEU A:871 , GLU A:905 , ALA A:906 , THR A:908 , HIS A:993 , 5AD A:1102binding site for residue B12 A 1101
02AC2SOFTWAREPHE A:598 , GLY A:600 , TYR A:779 , GLN A:865 , GLY A:868 , ASN A:901 , GLU A:905 , THR A:909 , PRO A:910 , B12 A:1101binding site for residue 5AD A 1102
03AC3SOFTWAREGLY A:219 , ALA A:220 , GLY A:221 , LYS A:222 , SER A:223 , SER A:224 , 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:1104binding site for residue GDP A 1103
04AC4SOFTWARESER A:223 , ASP A:262 , GLU A:310 , GDP A:1103 , MG A:1105binding site for residue MG A 1104
05AC5SOFTWAREILE A:248 , ASP A:249 , ASP A:262 , GLU A:310 , THR A:311 , MG A:1104binding site for residue MG A 1105
06AC6SOFTWAREARG A:231binding site for residue ACT A 1106
07AC7SOFTWAREGLY B:38 , HIS B:39 , ASP B:40 , ALA B:41 , SER B:42 , MET B:46 , ALA B:82 , TYR B:86 , GLN B:87 , GLY B:114 , GLY B:116 , TYR B:136 , SER B:137 , PRO B:138 , GLY B:141 , MET B:149 , GLY B:741 , GLN B:742 , HIS B:780binding site for residue B12 B 1101
08AC8SOFTWAREGLY B:219 , ALA B:220 , GLY B:221 , LYS B:222 , SER B:223 , SER B:224 , ARG B:265 , GLU B:310 , 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
09AC9SOFTWARESER B:223 , ASP B:262 , GLU B:310 , GDP B:1102 , MG B:1104binding site for residue MG B 1103
10AD1SOFTWAREILE B:248 , ASP B:249 , ASP B:262 , GLU B:310 , THR B:311 , MG B:1103binding site for residue MG B 1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XC6)

(-) 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 4XC6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XC6)

(-) Exons   (0, 0)

(no "Exon" information available for 4XC6)

(-) 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:1067
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee......hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee............hhhhh.......eeeeeee..........hhhhhhhhhhhh...eeeee..........hhhhh.eeeeee.....hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh....hhhhh.eee.......hhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....ee.eee.....eee........hhhhhhhhhhhh.........................ee...hhhhhhhhhhhhh.....eeeeee.hhhhhh......hhhhhh..........hhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.eee...hhhhhhh......hhhhhhhhhhhhhhhhhhh....ee.eeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc6 A   21 RGPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVVTAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIVPDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLDTVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGAGKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAINHPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAAIVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDVAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMSLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQAYSGDEYVVIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGSFPYTAGVFAFKREGEDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVSMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAYDEAITTPTAESVRRALAIQLIINREWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGDPTPQTLELARSSEDEKQSQLHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 1093
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530|      546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      1086       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       530|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        537                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:1061
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee......hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh....eeeeeee............hhhhh.......eeeeeee..........hhhhhhhhhhhh...eeeee..........hhhhh.eeeeee.....hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhhhhh....hhhhh.eee.......hhhhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee......eeee.eee.....eee........hhhhhhhhhhhh.......................eee...hhhhhhhhhhhhh.....eeeeee.hhhhhh......hhhhhh..........hhhhhhhhh.........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.eee....hhhhhh......hhhhhhhhhhhhhhhhhhh....ee..eeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeee..hhhhhhhhhhhhhhhhhhhhhh...hhhhhh.eeeeee........hhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhh.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4xc6 B   22 GPANKVRFVTAASLFDGHDASINIMRRILQSQGCEVIHLGHNRSVQEVVTAALQEDVQGIAISSYQGGHVEYFKYMIDLLREHGGEHIQVFGGGGGVIVPDEIRELQAYGVARIYSPEDGQRMGLAGMITDMAQRCDIDLTRYAPTTLDTVVAGDRRALAQLITALENGKADPELVSALHAQAKAAAVPVLGITGTGGAGKSSLTDELIRRFRLDQDDALSIAVISIDPSRRKSGGALLGDRIRMNAINHPNIFMRSLATREAGSEISQALPDVIAACKAARFDLVIVETSGIGQGDAAIVPHVDLSLYVMTPEFGAASQLEKIDMLDFADFVAINKFDRKGAQDAWRDVAKQVQRNREQWHSRAEDMPVYGTQASRFNDDGVTMLYQGLVGALGARGMSLKPGTLPNLEGRISTGQNVIVPPARSRYLAELADTVRAYHRRVVAQSKLARERQQLRAAHDMLQGAGHESAALETLASERDVSLGAVERKLLAMWPQMQQAYSGDEYVVKIRDKEIRTGLISTTLSGTKIRKVVLPRFEDEGEILKWLMRENVPGSFPYTAGVFAFKREGDPTRMFAGEGDAFRTNRRFKLVSEGMEAKRLSTAFDSVTLYGEDPHERPDIYGKVGNSGVSIATLEDMKVLYDGFDLTNPSTSVSMTINGPAPTILAMFMNTAIDQQIDRFRADNGRDPTADEEAKIRAWVLQNVRGTVQADILKEDQGQNTCIFSTEFSLKVMGDIQEYFVHHQVRNFYSVSISGYHIAEAGANPISQLAFTLANGFTYVEAYLARGMHIDDFAPNLSFFFSNGMDPEYSVLGRVARRIWAVTMRDKYGANDRSQKLKYHIQTSGRSLHAQEIDFNDIRTTLQALIAIYDNCNSLHTNAYDITTPTAESVRRALAIQLIINREWGVAKCENPNQGSFLIEELTDLVEEAVLQEFERIAERGGVLGAMETGYQRGKIQEESLYYEQLKHDGTLPIIGVNTFRNPNGLARSSEDEKQSQLHRLTEFHGAHQADAEAMLARLRQAVIDNRNVFAVLMDAVRVCSLGQITHALFEVGGQYRRNM 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       531       541       551       561       571       581       591|      602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902 ||    914       924       934       944       954       964       974       984       994      1004     |1022      1032      1042      1052      1062      1072      1082      1092 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   591|                                                                                                                                                                                                                                                                                                                    904|                                                                                                   1010|                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    593                                                                                                                                                                                                                                                                                                                     907                                                                                                    1019
   Legend:   → Mismatch (orange background)
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  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 4XC6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XC6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XC6)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4xc6
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  ICMF_CUPMC | Q1LRY0
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 Related Entries

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

UniProtKB/Swiss-Prot
        ICMF_CUPMC | Q1LRY0: 4xc7 4xc8 5cjt 5cju 5cjv 5cjw

(-) Related Entries Specified in the PDB File

4xc7 SAME PROTEIN WITHOUT BOUND ADENOSYLCOBALAMIN AND WITH BOUND GDP
4xc8 SAME PROTEIN WITH BOUND ADENOSYLCOBALAMIN AND GDP