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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-HYDROXYISOBUTYRYL-COA MUTASE
 
Authors :  M. Zahn, N. Kurteva-Yaneva, T. Rohwerder, N. Straeter
Date :  18 Aug 14  (Deposition) - 11 Mar 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (2x)
Biol. Unit 2:  B,D  (2x)
Keywords :  Tim Rossmann Fold, Mutase, Coa, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Kurteva-Yaneva, M. Zahn, M. T. Weichler, R. Starke, H. Harms, R. H. Muller, N. Strater, T. Rohwerder
Structural Basis Of The Stereospecificity Of Bacterial B12-Dependent 2-Hydroxyisobutyryl-Coa Mutase.
J. Biol. Chem. V. 290 9727 2015
PubMed-ID: 25720495  |  Reference-DOI: 10.1074/JBC.M115.645689

(-) Compounds

Molecule 1 - 2-HYDROXYISOBUTYRYL-COA MUTASE LARGE SUBUNIT
    ChainsA, B
    EC Number5.4.99.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneHCMA
    Organism ScientificAQUINCOLA TERTIARICARBONIS
    Organism Taxid391953
 
Molecule 2 - 2-HYDROXYISOBUTYRYL-COA MUTASE SMALL SUBUNIT
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneHCMB
    Organism ScientificAQUINCOLA TERTIARICARBONIS
    Organism Taxid391953

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)A C 
Biological Unit 2 (2x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
13HC2Ligand/Ion3-HYDROXYBUTANOYL-COENZYME A
23KK2Ligand/IonS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-3,5,9-TRIHYDROXY-8,8-DIMETHYL-3,5-DIOXIDO-10,14-DIOXO-2,4,6-TRIOXA-11,15-DIAZA-3LAMBDA~5~,5LAMBDA~5~-DIPHOSPHAHEPTADECAN-17-YL} 2-HYDROXY-2-METHYLPROPANETHIOATE
35AD1Ligand/Ion5'-DEOXYADENOSINE
4B122Ligand/IonCOBALAMIN
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
13HC2Ligand/Ion3-HYDROXYBUTANOYL-COENZYME A
23KK2Ligand/IonS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-3,5,9-TRIHYDROXY-8,8-DIMETHYL-3,5-DIOXIDO-10,14-DIOXO-2,4,6-TRIOXA-11,15-DIAZA-3LAMBDA~5~,5LAMBDA~5~-DIPHOSPHAHEPTADECAN-17-YL} 2-HYDROXY-2-METHYLPROPANETHIOATE
35AD2Ligand/Ion5'-DEOXYADENOSINE
4B122Ligand/IonCOBALAMIN
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
13HC2Ligand/Ion3-HYDROXYBUTANOYL-COENZYME A
23KK2Ligand/IonS-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]-3,5,9-TRIHYDROXY-8,8-DIMETHYL-3,5-DIOXIDO-10,14-DIOXO-2,4,6-TRIOXA-11,15-DIAZA-3LAMBDA~5~,5LAMBDA~5~-DIPHOSPHAHEPTADECAN-17-YL} 2-HYDROXY-2-METHYLPROPANETHIOATE
35AD-1Ligand/Ion5'-DEOXYADENOSINE
4B122Ligand/IonCOBALAMIN

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:27 , TYR A:76 , THR A:78 , MET A:79 , SER A:82 , ARG A:83 , THR A:86 , ARG A:88 , ILE A:90 , SER A:115 , ASP A:117 , SER A:165 , THR A:167 , THR A:196 , GLN A:198 , GLN A:208 , ARG A:235 , ASN A:237 , ASN A:240 , TYR A:244 , HIS A:245 , ARG A:284 , ALA A:286 , PHE A:288 , ARG A:328 , PHE A:329 , HIS A:330 , GLN A:332 , GLN A:363 , SER A:364 , 5AD A:803 , HOH A:911 , HOH A:917 , HOH A:939 , HOH A:945 , HOH A:977 , HOH A:999 , HOH A:1006 , HOH A:1009 , HOH A:1021 , HOH A:1054 , B12 C:800BINDING SITE FOR RESIDUE 3HC A 801
2AC2SOFTWAREPHE A:27 , TYR A:76 , THR A:78 , MET A:79 , SER A:82 , ARG A:83 , THR A:86 , ARG A:88 , ILE A:90 , SER A:115 , ASP A:117 , SER A:165 , THR A:167 , THR A:196 , GLN A:198 , GLN A:208 , ARG A:235 , ASN A:237 , ASN A:240 , TYR A:244 , HIS A:245 , ARG A:284 , ALA A:286 , PHE A:288 , ARG A:328 , PHE A:329 , HIS A:330 , GLN A:332 , GLN A:363 , SER A:364 , 5AD A:803 , HOH A:911 , HOH A:917 , HOH A:939 , HOH A:945 , HOH A:977 , HOH A:999 , HOH A:1006 , HOH A:1009 , HOH A:1021 , B12 C:800BINDING SITE FOR RESIDUE 3KK A 802
3AC3SOFTWAREILE A:90 , GLY A:92 , ASP A:117 , GLU A:140 , TYR A:244 , GLN A:332 , ALA A:335 , ASN A:368 , GLU A:372 , ILE A:376 , PRO A:377 , 3HC A:801 , 3KK A:802 , HOH A:923 , HOH A:978 , HOH A:1052 , HOH A:1053 , HOH A:1054 , HOH A:1056 , HOH A:1057 , B12 C:800 , HOH C:938BINDING SITE FOR RESIDUE 5AD A 803
4AC4SOFTWAREPHE B:27 , ALA B:31 , TYR B:76 , THR B:78 , MET B:79 , SER B:82 , ARG B:83 , THR B:86 , ARG B:88 , ILE B:90 , SER B:115 , ASP B:117 , SER B:165 , THR B:167 , THR B:196 , GLN B:198 , GLN B:208 , ARG B:235 , ASN B:237 , ASN B:240 , TYR B:244 , HIS B:245 , ARG B:284 , ALA B:286 , PHE B:288 , ARG B:328 , PHE B:329 , HIS B:330 , GLN B:332 , GLN B:363 , SER B:364 , B12 D:800BINDING SITE FOR RESIDUE 3HC B 801
5AC5SOFTWAREPHE B:27 , TYR B:76 , THR B:78 , MET B:79 , SER B:82 , ARG B:83 , THR B:86 , ARG B:88 , ILE B:90 , SER B:115 , ASP B:117 , SER B:165 , THR B:167 , THR B:196 , GLN B:198 , GLN B:208 , ARG B:235 , ASN B:237 , ASN B:240 , TYR B:244 , HIS B:245 , ARG B:284 , ALA B:286 , PHE B:288 , ARG B:328 , PHE B:329 , HIS B:330 , GLN B:332 , GLN B:363 , SER B:364 , B12 D:800BINDING SITE FOR RESIDUE 3KK B 802
6AC6SOFTWAREASP A:117 , PHE A:118 , MET A:120 , LEU A:123 , GLU A:140 , ALA A:207 , GLN A:208 , GLU A:210 , GLU A:248 , ALA A:249 , ALA A:335 , GLU A:372 , ALA A:373 , ALA A:375 , ILE A:376 , 3HC A:801 , 3KK A:802 , 5AD A:803 , HOH A:903 , HOH A:910 , GLY C:17 , HIS C:18 , ASP C:19 , ARG C:20 , GLY C:21 , VAL C:25 , GLY C:61 , VAL C:62 , SER C:63 , LEU C:65 , GLY C:67 , ILE C:91 , ALA C:92 , GLY C:93 , GLY C:94 , LEU C:113 , LEU C:114 , GLN C:115 , THR C:117 , ILE C:122 , HOH C:904 , HOH C:905 , HOH C:907 , HOH C:910 , HOH C:922 , HOH C:936 , HOH C:938BINDING SITE FOR RESIDUE B12 C 800
7AC7SOFTWAREASP B:117 , PHE B:118 , MET B:120 , LEU B:123 , GLU B:140 , ALA B:207 , GLN B:208 , GLU B:210 , GLU B:248 , ALA B:249 , ALA B:335 , GLU B:372 , ALA B:373 , ALA B:375 , ILE B:376 , 3HC B:801 , 3KK B:802 , GLY D:17 , HIS D:18 , ASP D:19 , ARG D:20 , GLY D:21 , VAL D:25 , GLY D:61 , VAL D:62 , SER D:63 , LEU D:65 , GLY D:67 , ILE D:91 , GLY D:93 , GLY D:94 , LEU D:113 , LEU D:114 , GLN D:115 , THR D:117 , ILE D:122 , HOH D:901BINDING SITE FOR RESIDUE B12 D 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R3U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:69 -Pro A:70
2Tyr B:69 -Pro B:70

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R3U)

(-) Exons   (0, 0)

(no "Exon" information available for 4R3U)

(-) 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:557
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.....ee....hhhhhh..hhhhh..............hhhhh...ee..ee...hhhhhhhhhhhhhhh....eeee.hhhhhhh....hhhhh...........hhhhhhhhh.........eeee...hhhhhhhhhhhhhhhh..hhhhh.eee...hhhhhhh......hhhhhhhhhhhhhhhhhhhh..ee...eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh....hhhhh...eeeee.hhhh...hhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3u A   2 TWLEPQIKSQLQSERKDWEANEVGAFLKKAPERKEQFHTIGDFPVQRTYTAADIADTPLEDIGLPGRYPFTRGPYPTMYRSRTWTMRQIAGFGTGEDTNKRFKYLIAQGQTGISTDFDMPTLMGYDSDHPMSDGEVGREGVAIDTLADMEALLADIDLEKISVSFTINPSAWILLAMYVALGEKRGYDLNKLSGTVQADILKEYMAQKEYIYPIAPSVRIVRDIITYSAKNLKRYNPINISGYHISEAGSSPLQEAAFTLANLITYVNEVTKTGMHVDEFAPRLAFFFVSQGDFFEEVAKFRALRRCYAKIMKERFGARNPESMRLRFHCQTAAATLTKPQYMVNVVRTSLQALSAVLGGAQSLHTNGYDEAFAIPTEDAMKMALRTQQIIAEESGVADVIDPLGGSYYVEALTTEYEKKIFEILEEVEKRGGTIKLIEQGWFQKQIADFAYETALRKQSGQKPVIGVNRFVENEEDVKIEIHPYDNTTAERQISRTRRVRAERDEAKVQAMLDQLVAVAKDESQNLMPLTIELVKAGATMGDIVEKLKGIWGTYRE 558
                                    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       451       461       471       481       491       501       511       521       531       541       551       

Chain B from PDB  Type:PROTEIN  Length:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.....ee....hhhhhh..hhhhh..............hhhhh...ee..ee...hhhhhhhhhhhhhhh....eeee.hhhhhh.....hhhhh...........hhhhhhhhh.........eeee...hhhhhhhhhhhhhhhhh.hhhhh.eee...hhhhhhh......hhhhhhhhhhhhhhhhhhhh..ee...eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh....hhhhh...eeeee.hhhh...hhhhhhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3u B   2 TWLEPQIKSQLQSERKDWEANEVGAFLKKAPERKEQFHTIGDFPVQRTYTAADIADTPLEDIGLPGRYPFTRGPYPTMYRSRTWTMRQIAGFGTGEDTNKRFKYLIAQGQTGISTDFDMPTLMGYDSDHPMSDGEVGREGVAIDTLADMEALLADIDLEKISVSFTINPSAWILLAMYVALGEKRGYDLNKLSGTVQADILKEYMAQKEYIYPIAPSVRIVRDIITYSAKNLKRYNPINISGYHISEAGSSPLQEAAFTLANLITYVNEVTKTGMHVDEFAPRLAFFFVSQGDFFEEVAKFRALRRCYAKIMKERFGARNPESMRLRFHCQTAAATLTKPQYMVNVVRTSLQALSAVLGGAQSLHTNGYDEAFAIPTEDAMKMALRTQQIIAEESGVADVIDPLGGSYYVEALTTEYEKKIFEILEEVEKRGGTIKLIEQGWFQKQIADFAYETALRKQSGQKPVIGVNRFVENEVKIEIHPYDNTTAERQISRTRRVRAERDEAKVQAMLDQLVAVAKDESQNLMPLTIELVKAGATMGDIVEKLKGIWGTYRE 558
                                    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       451       461       471    || 483       493       503       513       523       533       543       553     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    476|                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     479                                                                               

Chain C from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3u C   3 QTPIRVLLAKVGLDGHDRGVKVVARALRDAGMDVIYSGLHRTPEEVVNTAIQEDVDVLGVSLLSGVQLTVFPKIFKLLDERGAGDLIVIAGGVMPDEDAAAIRKLGVREVLLQDTPPQAIIDSIRSLVAAR 133
                                    12        22        32        42        52        62        72        82        92       102       112       122       132 

Chain D from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r3u D   4 TPIRVLLAKVGLDGHDRGVKVVARALRDAGMDVIYSGLHRTPEEVVNTAIQEDVDVLGVSLLSGVQLTVFPKIFKLLDERGAGDLIVIAGGVMPDEDAAAIRKLGVREVLLQDTPPQAIIDSIRSLVAA 132
                                    13        23        33        43        53        63        73        83        93       103       113       123         

   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 4R3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R3U)

(-) Gene Ontology  (7, 9)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

2xiq 4req