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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND BOUND TO THDP AND MN2+
 
Authors :  J. M. Johnston, E. N. M. Jirgis, G. Bashiri, E. M. M. Bulloch, E. N. Baker
Date :  16 Nov 15  (Deposition) - 22 Jun 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Menaquinone Biosynthesis, Mend, 2-Succinyl-5-Enolpyruvyl-6-Hydroxy-3- Cyclohexadiene-1-Carboxylate Synthase, Thiamin-Diphosphate Dependent Enzyme, Pyruvate Oxidase Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. N. Jirgis, G. Bashiri, E. M. Bulloch, J. M. Johnston, E. N. Baker
Structural Views Along The Mycobacterium Tuberculosis Mend Reaction Pathway Illuminate Key Aspects Of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Structure V. 24 1167 2016
PubMed-ID: 27291649  |  Reference-DOI: 10.1016/J.STR.2016.04.018

(-) Compounds

Molecule 1 - 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1- CARBOXYLATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.2.1.9
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS
    Expression System Taxid: 1772
    Gene: MEND, RV0555
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Other Details: PROTEIN WAS PURIFIED WITH AN N-TERMINAL HIS-TAG THAT IS NOT VISIBLE IN THE CRYSTAL STRUCTURE. THE NUMBERING OF THE PDB FILE MATCHES THE NUMBERING OF THE SEQUENCE FROM THE BIOLOGICAL START RESIDUE (E.G. M 1 IN SEQUENCE = M 1 IN PDB FILE).
    Strain: ATCC 25618 / H37RV
    Synonym: SEPHCHC SYNTHASE,MENAQUINONE BIOSYNTHESIS PROTEIN MEND

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2TDP4Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:440 , ASP A:469 , GLY A:471 , TDP A:602 , HOH A:728binding site for residue MN A 601
2AC2SOFTWARESER A:377 , ASN A:378 , PRO A:379 , ILE A:404 , GLY A:439 , ASP A:440 , LEU A:441 , THR A:442 , ASP A:469 , GLY A:471 , GLY A:473 , ILE A:474 , PHE A:493 , MN A:601 , HOH A:728 , HOH A:732 , SER D:29binding site for residue TDP A 602
3AC3SOFTWARESER B:377 , ASN B:378 , PRO B:379 , GLY B:439 , ASP B:440 , LEU B:441 , THR B:442 , ASP B:469 , GLY B:471 , GLY B:472 , GLY B:473 , PHE B:493 , MN B:602 , HOH B:709 , HOH B:715 , PRO C:27 , GLY C:28binding site for residue TDP B 601
4AC4SOFTWAREASP B:440 , ASP B:469 , GLY B:471 , TDP B:601 , HOH B:709binding site for residue MN B 602
5AC5SOFTWAREPRO B:27 , GLU B:55 , GLN B:118 , SER C:377 , ASN C:378 , PRO C:379 , ALA C:402 , GLY C:403 , ILE C:404 , ASP C:405 , GLY C:439 , ASP C:440 , LEU C:441 , THR C:442 , ASP C:469 , GLY C:471 , GLY C:472 , GLY C:473 , ILE C:474 , PHE C:475 , MN C:602 , HOH C:728binding site for residue TDP C 601
6AC6SOFTWAREASP C:440 , ASP C:469 , GLY C:471 , TDP C:601 , HOH C:728binding site for residue MN C 602
7AC7SOFTWAREPRO A:27 , GLU A:55 , ALA A:82 , SER D:377 , ASN D:378 , PRO D:379 , ALA D:402 , GLY D:403 , ILE D:404 , GLY D:439 , ASP D:440 , LEU D:441 , THR D:442 , ASP D:469 , GLY D:471 , GLY D:472 , GLY D:473 , ILE D:474 , MN D:602 , HOH D:704 , HOH D:742 , HOH D:809binding site for residue TDP D 601
8AC8SOFTWAREASP D:440 , ASP D:469 , GLY D:471 , TDP D:601 , HOH D:704binding site for residue MN D 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:183 -Pro A:184
2Glu B:183 -Pro B:184
3Glu D:183 -Pro D:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ESD)

(-) 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:539
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.............hhhhh.eeee.........hhhhhhhhhhhhhhhhhhhhhh........eeeeee...........hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhh.....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhh..........eeeeeee...hhhhhhh.hhhhhhh......hhhhhhhhh..eeee.hhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5esd A   1 MNPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLREPLVPTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGGGIFELLSDVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      |198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478|      495       505       515       525       535       545         
                                                                                                                                                                                                                    187|                                                                                                                                                                                                                                                                                       478|                                                                    
                                                                                                                                                                                                                     196                                                                                                                                                                                                                                                                                        486                                                                    


Chain B from PDB  Type:PROTEIN  Length:532
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhh.............hhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...............hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhhh....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eee.........hhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhh..........eeeeeee......hhhhhhh.....hhhhhhhhh..eeeeehhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5esd B   1 MNPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLREPLVPDPEVTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGGGIVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190|      204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424||     439       449       459       469    || 492       502       512       522       532       542       552  
                                                                                                                                                                                                                       190|                                                                                                                                                                                                                                   425|                                        474|                                                                  
                                                                                                                                                                                                                        195                                                                                                                                                                                                                                    431                                         488                                                                  


Chain C from PDB  Type:PROTEIN  Length:540
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh..eeeee....................hhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee..........hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhhh....eeee..............eee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eee.........hhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhh..........eeeeeee...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..eeeeehhhhhhhhhhh.....eeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5esd C   2 NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLREVTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 ||    202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422   ||  434       444       454       464       474       484       494       504       514       524       534       544       554
                                                                                                                                                                                                               183|                                                                                                                                                                                                                                    426|                                                                                                                             
                                                                                                                                                                                                                195                                                                                                                                                                                                                                     429                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeee........hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh..eeeee....................hhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee...........hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhhh....eeee..............eee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eee.........hhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhh..........eeeeeee....hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..eeee.hhhhhhhhhhh.....eeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5esd D   2 NPSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTGANQTMEQLGYFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLREPVTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGGGIFELLEQGDPRFSDVSSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  ||   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421     ||433       443       453       463       473       483       493       503       513       523       533       543       553 
                                                                                                                                                                                                                184|                                                                                                                                                                                                                                     427|                                                                                                                            
                                                                                                                                                                                                                 195                                                                                                                                                                                                                                      430
   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 5ESD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  5esd
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  2.2.1.9
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 Related Entries

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

UniProtKB/Swiss-Prot
        MEND_MYCTU | P9WK11: 5erx 5ery 5eso 5ess 5esu

(-) Related Entries Specified in the PDB File

5erx 5ery 5eso 5ess 5esu