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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS WILD-TYPE MALATE SYNTHASE IN COMPLEX WITH PRODUCT MALATE
 
Authors :  I. V. Krieger, H. -L. Huang, J. C. Sacchettini
Date :  23 Dec 15  (Deposition) - 26 Oct 16  (Release) - 11 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Huang, I. V. Krieger, M. K. Parai, V. B. Gawandi, J. C. Sacchettini
Mycobacterium Tuberculosis Malate Synthase Structures With Fragments Reveal A Portal For Substrate/Product Exchange.
J. Biol. Chem. V. 291 27421 2016
PubMed-ID: 27738104  |  Reference-DOI: 10.1074/JBC.M116.750877
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MALATE SYNTHASE G
    Chains: A, B
    EC Number: 2.3.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: GLCB, RV1837C, MTCY1A11.06
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Other Details: REGIONS CONTAINING RESIDUES 1-2, 304-308, AND 728-741 ARE DISORDERED AND EXCLUDED FROM THE FINAL REFINED MODEL.
    Strain: ATCC 25618 / H37RV

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GLV1Ligand/IonGLYOXYLIC ACID
2LMR1Ligand/Ion(2S)-2-HYDROXYBUTANEDIOIC ACID
3MG3Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GLV-1Ligand/IonGLYOXYLIC ACID
2LMR1Ligand/Ion(2S)-2-HYDROXYBUTANEDIOIC ACID
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GLV1Ligand/IonGLYOXYLIC ACID
2LMR-1Ligand/Ion(2S)-2-HYDROXYBUTANEDIOIC ACID
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:434 , ASP A:462 , LMR A:802 , HOH A:917binding site for residue MG A 801
2AC2SOFTWAREASP A:274 , ARG A:339 , GLU A:434 , GLY A:459 , PHE A:460 , LEU A:461 , ASP A:462 , TRP A:541 , ASP A:633 , ALA A:635 , MG A:801 , HOH A:912binding site for residue LMR A 802
3AC3SOFTWAREGLU B:434 , ASP B:462 , GLV B:803 , HOH B:903 , HOH B:917binding site for residue MG B 801
4AC4SOFTWAREGLN A:557 , HOH A:926 , ARG B:69 , HOH B:920binding site for residue MG B 802
5AC5SOFTWAREASP B:274 , ARG B:339 , GLU B:434 , GLY B:459 , PHE B:460 , LEU B:461 , ASP B:462 , TRP B:541 , MG B:801 , HOH B:903binding site for residue GLV B 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H8U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:683 -Pro A:684
2Ala B:683 -Pro B:684

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H8U)

(-) Exons   (0, 0)

(no "Exon" information available for 5H8U)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:720
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..eeehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.................hhhhhh..eeeeeee..hhhhhhhhhh..eeehhhhhhhh...............hhhhhhhhhhhhhhhhhhhh.....hhhhh.eeeee..eeeee....ee...hhh.eeeeee....eeeeeeee..eeeeeee.............eeeeeee...eeeee........hhhhhhhhhhhhhhhhhh..eee...eee....eeee.....eeee....eeeee......eeeeee.....eeehhhhhhhhhhhhhhhhhh...............eeee.....hhhhhhhhhhhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.....eeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5h8u A   3 DRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQALLNARDELQAQIDKWHRRRVIEPIDMDAYRQFLTEIGYLLPEPDDFTITTSGVDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETDGAEKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVALPDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDRAGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAAAVAFLRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFEGIMDALFTGLIAIHGLKASDVNGPLINSRTGSIYIVKPKMHGPAEVAFTCELFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGLAGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRWVDQGVGCSKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASLERMAPLVDRQNAGDVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPILHRRRREFKARAAE 727
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302||     317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727
                                                                                                                                                                                                                                                                                                                                      303|                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                                                                                                                       309                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:716
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.................hhhhhh....eeeee..hhhhhhhhhh..eeehhhhhhh.............hhhhhhhhhhhhhhhhhhhh.....hhhhh.eeeee..eeeee.........hhh.eeeeeee..eeeeeeeee..eeeeeee....hhhhh....eeeeeee...eeeee........hhhhhhhhhhhhhhhhhh..ee....ee....eeee.....eeee....eeeee...................hhhhhhhhhhhhhhhhhh................eeeee...hhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhh..hhhhhhhhh......hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh......eeee.....eeeehhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h8u B   3 DRVSVGNLRIARVLYDFVNNEALPGTDIDPDSFWAGVDKVVADLTPQNQALLNARDELQAQIDKWHRRRVIEPIDMDAYRQFLTEIGYLLPEPDDFTITTSGVDAEITTTAGPQLVVPVLNARFALNAANARWGSLYDALYGTDVIPETEKGPTYNKVRGDKVIAYARKFLDDSVPLSSGSFGDATGFTVQDGQLVVALPDKSTGLANPGQFAGYTGAAESPTSVLLINHGLHIEILIDPESQVGTTDRAGVKDVILESAITTIMDFEDSVAAVDAADKVLGYRNWLGLNKGDLAAAVFLRVLNRDRNYTAPGGGQFTLPGRSLMFVRNVGHLMTNDAIVDTDGSEVFEGIMDALFTGLIAIHGLKASDVNGPLINSRTGSIYIVKPKMHGPAEVAFTCELFSRVEDVLGLPQNTMKIGIMDEERRTTVNLKACIKAAADRVVFINTGFLDRTGDEIHTSMEAGPMVRKGTMKSQPWILAYEDHNVDAGLAAGFSGRAQVGKGMWTMTELMADMVETKIAQPRAGASTAWVPSPTAATLHALHYHQVDVAAVQQGLAGKRRATIEQLLTIPLAKELAWAPDEIREEVDNNCQSILGYVVRWVDQGVGCSKVPDIHDVALMEDRATLRISSQLLANWLRHGVITSADVRASLERMAPLVDRQNAGDVAYRPMAPNFDDSIAFLAAQELILSGAQQPNGYTEPILHRRRREFKARAAE 727
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721      
                                                                                                                                                                              151|                                                                                                                                                 303|                                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                                                                                                                                               155                                                                                                                                                  310
   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 5H8U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H8U)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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    Ala A:683 - Pro A:684   [ RasMol ]  
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  2.3.3.9
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 Related Entries

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UniProtKB/Swiss-Prot
        MASZ_MYCTU | P9WK17: 1n8i 1n8w 2gq3 3s9i 3s9z 3sad 3saz 3sb0 5c7v 5c9r 5c9u 5c9w 5c9x 5cah 5cak 5cbb 5cbi 5cbj 5cc3 5cc5 5cc6 5cc7 5ccz 5cew 5cjm 5cjn 5drc 5dri 5dx7 5e9x 5ecv 5h8m 5h8p 5t8g

(-) Related Entries Specified in the PDB File

5h8m 5h8p