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(-) Description

Title :  FUMARATE HYDRATASE OF MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH FORMATE
 
Authors :  M. Kasbekar, G. Fischer, B. T. Mott, A. Yasgar, M. Hyvonen, H. I. Boshoff C. E. Barry, C. J. Thomas
Date :  09 Dec 15  (Deposition) - 22 Jun 16  (Release) - 13 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydratase, Metabolism, Tuberculosis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kasbekar, G. Fischer, B. T. Mott, A. Yasgar, M. Hyvonen, H. I. Boshoff, C. Abell, C. E. Barry, C. J. Thomas
Selective Small Molecule Inhibitor Of The Mycobacterium Tuberculosis Fumarate Hydratase Reveals An Allosteric Regulatory Site.
Proc. Natl. Acad. Sci. Usa V. 113 7503 2016
PubMed-ID: 27325754  |  Reference-DOI: 10.1073/PNAS.1600630113

(-) Compounds

Molecule 1 - FUMARATE HYDRATASE CLASS II
    Chains: A, B, C, D
    EC Number: 4.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FUMC, FUM, MT1130
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN CDC 1551 / OSHKOSH)
    Organism Taxid: 83331
    Strain: CDC 1551 / OSHKOSH
    Synonym: FUMARASE C

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FMT4Ligand/IonFORMIC ACID
3PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:318 , MET A:321 , LYS A:324 , ASN A:326 , FMT A:502 , THR C:186 , HIS C:187 , ASN D:140 , HOH D:641binding site for residue FMT A 501
2AC2SOFTWARESER A:318 , SER A:319 , ILE A:320 , FMT A:501 , THR D:106 , SER D:138 , SER D:139 , HOH D:641binding site for residue FMT A 502
3AC3SOFTWAREGLN A:198binding site for residue CL A 503
4AC4SOFTWARELEU A:303 , LEU C:429binding site for residue PG4 A 504
5AC5SOFTWARESER B:318 , MET B:321 , LYS B:324 , ASN B:326 , ASN C:140 , HOH C:556 , THR D:186 , HIS D:187binding site for residue FMT B 501
6AC6SOFTWARESER B:318 , SER B:319 , ILE B:320 , THR C:106 , SER C:138 , SER C:139binding site for residue FMT B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F92)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Thr A:16 -Met A:17
2Gly A:301 -Pro A:302
3Gly B:18 -Glu B:19
4Gly B:301 -Pro B:302
5Gly C:301 -Pro C:302
6Gln C:315 -Pro C:316
7Gly D:301 -Pro D:302
8Gln D:315 -Pro D:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F92)

(-) Exons   (0, 0)

(no "Exon" information available for 5F92)

(-) 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:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee...............hhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee................hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f92 A  10 YRIEHDTMGEVRVPAKALWRAQTQRAVENFPISGRGLERTQIRALGLLKGACAQVNSDLGLLAPEKADAIIAAAAEIADGQHDDQFPIDVFQTGSGTSSNMNTNEVIASIAAKGGVTLHPNDDVNMSQSSNDTFPTATHIAATEAAVAHLIPALQQLHDALAAKALDWHTVVKSGRTHLMDAVPVTLGQEFSGYARQIEAGIERVRACLPRLGELAIGGTAVGTGLNAPDDFGVRVVAVLVAQTGLSELRTAANSFEAQAARDGLVEASGALRTIAVSLTKIANDIRWMGSGPLTGLAEIQLPDLQPGSSIMPGKVNPVLPEAVTQVAAQVIGNDAAIAWGGANGAFELNVYIPMMARNILESFKLLTNVSRLFAQRCIAGLTANVEHLRRLAESSPSIVTPLNSAIGYEEAAAVAKQALKERKTIRQTVIDRGLIGDRLSIEDLDRRLDVLAMAKAEQL 469
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469


Chain B from PDB  Type:PROTEIN  Length:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eee......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee...............hhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee................hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.......hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f92 B  10 YRIEHMGEVRVPAKALWRAQTQRAVENFPISGRGLERTQIRALGLLKGACAQVNSDLGLLAPEKADAIIAAAAEIADGQHDDQFPIDVFQTGSGTSSNMNTNEVIASIAAKGGVTLHPNDDVNMSQSSNDTFPTATHIAATEAAVAHLIPALQQLHDALAAKALDWHTVVKSGRTHLMDAVPVTLGQEFSGYARQIEAGIERVRACLPRLGELAIGGTAVGTGLNAPDDFGVRVVAVLVAQTGLSELRTAANSFEAQAARDGLVEASGALRTIAVSLTKIANDIRWMGSGPLTGLAEIQLPDLQPGSSIMPGKVNPVLPEAVTQVAAQVIGNDAAIAWGGANGAFELNVYIPMMARNILESFKLLTNVSRLFAQRCIAGLTANVEHLRRLAESSPSIVTPLNSAIGYEEAAAVAKQALKERKTIRQTVIDRGLIGDRLSIEDLDRRLDVLAMAKAEQLDSD 472
                                ||  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 
                               14|                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                17                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee...............hhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f92 C   7 SANYRIEHDTMGEVRVPAKALWRAQTQRAVENFPISGRGLERTQIRALGLLKGACAQVNSDLGLLAPEKADAIIAAAAEIADGQHDDQFPIDVFQTGSGTSSNMNTNEVIASIAAKGGVTLHPNDDVNMSQSSNDTFPTATHIAATEAAVAHLIPALQQLHDALAAKALDWHTVVKSGRTHLMDAVPVTLGQEFSGYARQIEAGIERVRACLPRLGELAIGGTAVGTGLNAPDDFGVRVVAVLVAQTGLSELRTAANSFEAQAARDGLVEASGALRTIAVSLTKIANDIRWMGSGPLTGLAEIQLPDLQPGKVNPVLPEAVTQVAAQVIGNDAAIAWGGANGAFELNVYIPMMARNILESFKLLTNVSRLFAQRCIAGLTANVEHLRRLAESSPSIVTPLNSAIGYEEAAAVAKQALKERKTIRQTVIDRGLIGDRLSIEDLDRRLDVLAMAKA 466
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316|      332       342       352       362       372       382       392       402       412       422       432       442       452       462    
                                                                                                                                                                                                                                                                                                                                               316|                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                323                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:455
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee...............hhhhhhhhhhhhhhh....ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.......hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f92 D   8 ANYRIEHDTMGEVRVPAKALWRAQTQRAVENFPISGRGLERTQIRALGLLKGACAQVNSDLGLLAPEKADAIIAAAAEIADGQHDDQFPIDVFQTGSGTSSNMNTNEVIASIAAKGGVTLHPNDDVNMSQSSNDTFPTATHIAATEAAVAHLIPALQQLHDALAAKALDWHTVVKSGRTHLMDAVPVTLGQEFSGYARQIEAGIERVRACLPRLGELAIGGTAVGTGLNAPDDFGVRVVAVLVAQTGLSELRTAANSFEAQAARDGLVEASGALRTIAVSLTKIANDIRWMGSGPLTGLAEIQLPDLQPKVNPVLPEAVTQVAAQVIGNDAAIAWGGANGAFELNVYIPMMARNILESFKLLTNVSRLFAQRCIAGLTANVEHLRRLAESSPSIVTPLNSAIGYEEAAAVAKQALKERKTIRQTVIDRGLIGDRLSIEDLDRRLDVLAMAKAEQL 469
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464     
                                                                                                                                                                                                                                                                                                                                              316|                                                                                                                                                 
                                                                                                                                                                                                                                                                                                                                               324
   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 5F92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F92)

(-) Gene Ontology  (14, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  5f92
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  FUMC_MYCTO | P9WN92
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  FUMC_MYCTU | P9WN93
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  4.2.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        FUMC_MYCTO | P9WN92: 3no9 4adl 4adm 4apa 4apb 5f91
        FUMC_MYCTU | P9WN93: 3no9 4adl 4adm 4apa 4apb 5f91

(-) Related Entries Specified in the PDB File

5f91