Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF APO MEND FROM M. TUBERCULOSIS - P212121
 
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, Transferase (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, D, C, B
    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 CONTAINS AN N-TERMINAL HISTIDINE TAG FROM CLONING. THIS TAG IS NOT SEEN IN THE CRYSTAL STRUCTURE. THE PROTEIN IS NUMBERED AS IT WOULD BE IN THE NATIVE SEQUENCE.
    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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5ERY)

(-) Sites  (0, 0)

(no "Site" information available for 5ERY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ERY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ERY)

(-) 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:504
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh..eeeee..hhhhhhh..........eeee.....hhhhhhhhhhhhhhhhhhhh........eeee........hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhh.....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhhh..........eeeeeee...hhhhh....hhhhhhhhhh.eeeeehhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ery A   3 PSTTQARVVVDELIRGGVRDVVLCPGSAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTGGYFGTQVRASISLGLATSALNATWRSATCRVLAAATGARTANAGPVHFDIPLRTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGDVSSRPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    12        22      ||34        44        54        64        74        84        94       104       114||     132      |148       158       168       178   ||  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|   || 500       510       520       530       540       550    
                                                     29|                                                                                115|            139|                                 182|                                                                                                                                                                                                                                                                                471| 491|                                                          
                                                      32                                                                                 124             146                                  196                                                                                                                                                                                                                                                                                 487  496                                                          


Chain B from PDB  Type:PROTEIN  Length:496
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh..eeeeeeehhhhhhh........eee.........hhhhhhhhhhhhhhhhhhhhhh........eeeeee.....hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhhh....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....eeee..hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhh..........eeeeeee......hhhhhhhhh..eeee.hhhhhhhhhhh....eeeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ery B   3 PSTTQARVVVDELIRGGVRDVVLCPAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLGTFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPLTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    12        22    ||  36        46        56        66        76        86        96       106       127       137       147       157       167       177   ||  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       498       508       518       528       538       548      
                                                   27|                                                                               114|                                                    181|                                                                                                                                                                                                                                    427|                                      471|                                                         
                                                    32                                                                                126                                                     196                                                                                                                                                                                                                                     430                                       497                                                         


Chain C from PDB  Type:PROTEIN  Length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh..eeeee........hhhhh.eeee.....hhhhhhhhhhhhhhhhhhhh........eeee.......hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhh.....eeee............eeeee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhh..........eeeeee......hhhhhhhhh..eeeeehhhhhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ery C   3 PSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSANRPYELLFGTQVRASISLGLATSALNATWRSATCRVLAAATGARTANAGPVHFDIPLTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVK 537
                                    12        22        32        42        52        62        72        82        92       102       112|      135   ||  151       161       171       181|      205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425|      438       448       458       468||     504       514       524       534   
                                                                                                                                       112|          139|                                181|                                                                                                                                                                                                                                  425|                                     469|                                         
                                                                                                                                        126           146                                 196                                                                                                                                                                                                                                   429                                      496                                         


Chain D from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhh..eeeeehhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhhhhh........eeee......hhhhh........eee.eeeee....eeeee......hhhhh...eee............hhhhhhhh...eeeee.....hhhhhhhhhh....eeee..............eee.eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....eeee..hhhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhh.........eeeeeehhhhhhhhhhhh.........eeeeeeee.............hhhhhhhhh..eeee.hhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ery D   3 PSTTQARVVVDELIRGGVRDVVLCPGSRNAPLAFALQDADRSGRIRLHVRIDERTAGYLAIGLAIGAGAPVCVAMTSGTAVANLGPAVVEANYARVPLIVLSFGTQVRASISLGLAEDAPERTSALNATWRSATCRVLAAATGARTANAGPVHFDIPTPPGRPAGKPWTYTPPVTFDQPLDIDLSVDTVVISGHGAGVHPNLAALPTVAEPTAPRSGDNPLHPLALPLLRPQQVIMLGRPTLHRPVSVLLADAEVPVFALTTGPRWPDVSGNSQATGTRAVTTGAPRPAWLDRCAAMNRHAIAAVREQLAAHPLTTGLHVAAAVSHALRPGDQLVLGASNPVRDVALAGLDTRGIRVRSNRGVAGIDGTVSTAIGAALAYEGAHERTGSPDSPPRTIALIGDLTFVHDSSGLLIGPTEPIPRSLTIVVSNDNGSRIFGTPHDVDVGALCRAYHVESRQIEVDELGPTLDQPGAGMRVLEVKADRSSLRQLHAAIKAAL 554
                                    12        22        32        42        52        62        72        82        92       102 ||    133       143       153       163       173      |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  ||   496       506       516       526       536       546        
                                                                                                                               104|                                                   180|                                                                                                                                                                                                                                                                                471|                                                                
                                                                                                                                126                                                    196                                                                                                                                                                                                                                                                                 490
   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 5ERY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5ery)
 
  Sites
(no "Sites" information available for 5ery)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ery)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ery
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MEND_MYCTU | P9WK11
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.2.1.9
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MEND_MYCTU | P9WK11
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

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

(-) Related Entries Specified in the PDB File

5erx