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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRROLIDINE AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.
 
Authors :  D. O. Somers
Date :  08 Jun 15  (Deposition) - 01 Jul 15  (Release) - 07 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fold Type Iv, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Bertrand, N. Ancellin, B. Beaufils, R. P. Bingham, J. A. Borthwick, A. B. Boullay, E. Boursier, P. S. Carter, C. W. Chung, I. Churcher, N. Dodic, M. H. Fouchet, C. Fournier, P. L. Francis, L. A. Gummer, K. Herry, A. Hobbs, C. I. Hobbs, P. Homes, C. Jamieson, E. Nicodeme, S. D. Pickett, I. H. Reid, G. L. Simpson, L. A. Sloan, S. E. Smith, D. O. Somers, C. Spitzfaden, C. J. Suckling, K. Valko, Y. Washio, R. J. Young
The Discovery Of In Vivo Active Mitochondrial Branched-Chai Aminotransferase (Bcatm) Inhibitors By Hybridizing Fragment And Hts Hits.
J. Med. Chem. V. 58 7140 2015
PubMed-ID: 26090771  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00313

(-) Compounds

Molecule 1 - BRANCHED-CHAIN-AMINO-ACID AMINOTRANSFERASE, MITOCHONDRIAL
    Chains: A, B
    EC Number: 2.6.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Taxid: 562
    Fragment: RESIDUES 28-392
    Gene: BCAT2, BCATM, BCT2, ECA40
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCAT(M),PLACENTAL PROTEIN 18,PP18

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
14W62Ligand/Ion7-OXO-2-[2-OXO-2-(PYRROLIDIN-1-YL)ETHYL]-5-PROPYL-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
2CL2Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4EDO14Ligand/Ion1,2-ETHANEDIOL
5GOL2Ligand/IonGLYCEROL
6PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , ARG A:192 , LYS A:202 , TYR A:207 , GLU A:237 , THR A:240 , ASN A:242 , LEU A:266 , GLY A:268 , VAL A:269 , VAL A:270 , GLY A:312 , THR A:313 , HOH A:536 , HOH A:644 , HOH A:651binding site for residue PLP A 401
02AC2SOFTWARETYR A:141 , ARG A:143 , GLN A:224 , VAL A:238 , THR A:240 , MET A:241 , ALA A:314 , CYS A:315 , CYS A:318 , EDO A:403 , HOH A:661 , HOH A:665 , HOH A:679 , LEU B:153 , GLY B:154 , VAL B:155binding site for residue 4W6 A 402
03AC3SOFTWAREPHE A:30 , CYS A:315 , 4W6 A:402binding site for residue EDO A 403
04AC4SOFTWARETHR A:280 , GLU A:348 , ARG A:357 , HIS A:359 , TRP A:361binding site for residue EDO A 404
05AC5SOFTWARETYR A:246 , ARG A:306 , LEU A:341 , ARG A:344binding site for residue EDO A 405
06AC6SOFTWAREGLU A:42 , LEU A:59 , THR A:60 , LEU A:162binding site for residue EDO A 406
07AC7SOFTWAREHIS A:249 , HOH A:596 , ASP B:85 , ARG B:89 , ILE B:356 , HOH B:541binding site for residue EDO A 407
08AC8SOFTWAREASN A:200 , LEU A:261 , GLY A:263 , PRO A:267 , HOH A:529 , HOH A:541 , HOH A:601binding site for residue EDO A 408
09AC9SOFTWARETRP A:94 , HOH A:502 , HOH A:527binding site for residue EDO A 409
10AD1SOFTWAREARG A:92 , TRP A:94 , HOH A:502 , HOH A:791binding site for residue CL A 410
11AD2SOFTWAREPRO A:260 , LEU A:261 , HOH A:554 , HOH A:654 , ALA B:358binding site for residue GOL A 411
12AD3SOFTWARELEU A:153 , VAL A:155 , PHE B:75 , TYR B:141 , ARG B:143 , GLN B:224 , VAL B:238 , THR B:240 , MET B:241 , ALA B:314 , CYS B:315 , CYS B:318 , EDO B:404 , HOH B:686 , HOH B:707binding site for residue 4W6 B 402
13AD4SOFTWAREGLU B:42 , LEU B:59 , THR B:60 , LEU B:162 , HOH B:660binding site for residue DMS B 403
14AD5SOFTWAREPHE B:30 , 4W6 B:402 , HOH B:516binding site for residue EDO B 404
15AD6SOFTWAREASP B:276 , THR B:280 , GLU B:348 , HIS B:359 , TRP B:361 , HOH B:636binding site for residue EDO B 405
16AD7SOFTWARETYR B:246 , ARG B:306 , GLU B:340 , ARG B:344 , HOH B:593binding site for residue EDO B 406
17AD8SOFTWARELEU B:10 , GLN B:11 , LEU B:12 , HOH B:551binding site for residue EDO B 407
18AD9SOFTWAREGLU B:13 , GLN B:54 , GLN B:57 , HOH B:502 , HOH B:537binding site for residue EDO B 408
19AE1SOFTWAREASN B:200 , LEU B:261 , PRO B:267 , HOH B:523 , HOH B:604binding site for residue EDO B 409
20AE2SOFTWAREHIS B:233 , MET B:293 , LYS B:294 , TYR B:325binding site for residue EDO B 410
21AE3SOFTWAREARG B:92 , TRP B:94 , HOH B:667 , HOH B:729binding site for residue CL B 411
22AE4SOFTWAREHOH B:588 , HOH B:597 , HOH B:729binding site for residue GOL B 412
23AE5SOFTWARELEU B:74 , PHE B:75 , ARG B:99 , SER B:103 , ARG B:192 , TYR B:201 , LEU B:203 , TYR B:207 , GLU B:237 , THR B:240 , ASN B:242 , LEU B:266 , GLY B:268 , VAL B:269 , VAL B:270 , GLY B:312 , THR B:313 , HOH B:543 , HOH B:559 , HOH B:645binding site for Di-peptide PLP B 401 and LYS B 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:338 -Pro A:339
2Gly B:338 -Pro B:339

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWW)

(-) 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:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhee.....................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee....eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bww A   3 SSFKAADLQLEMTQKPHKKPGPLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    12        22||      35        45        55        65        75        85        95       105       115       125       135       145       155       165     ||182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
                                               23|                                                                                                                                             171|                                                                                                                                                                                          
                                                27                                                                                                                                              179                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhee....................eeeeeeee..ee...eeee...eee...hhhhhh..eee..eeeee.....eeeehhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......eeeeeeeeee............eeeeeeeeee....eeeee................hhhhhhhhhhhhhhhhhh...eeeeee....eeeee..eeeeeeee.....eeeee.........hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhh..eeeeeeee...eeeeeeeeee..eeee..hhhhhhhhhhhhhhhhhhhhh.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bww B   2 SSSFKAADLQLEMTQKPHKKPGLVFGKTFTDHMLMVEWNDKGWGQPRIQPFQNLTLHPASSSLHYSLQLFEGMKAFKGKDQQVRLFRPWLNMDRMLRSAMRLCLPSFDKLELLECIRRLIEVDKDWVPDAAGTSLYVRPVLIGNEPSLGVSQPTRALLFVILCPVGVTPVSLLADPAFIRAWVGGVGNYKLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPLNGVILPGVVRQSLLDMAQTWGEFRVVERTITMKQLLRALEEGRVREVFGSGTACQVCPVHRILYKDRNLHIPTMENGPELILRFQKELKEIQYGIRAHEWMFPV 365
                                    11        21 ||     35        45        55        65        75        85        95       105       115       125       135       145       155       165     ||182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
                                                23|                                                                                                                                            171|                                                                                                                                                                                          
                                                 28                                                                                                                                             179
   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 5BWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  BCAT2_HUMAN | O15382
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  2.6.1.42
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 Related Entries

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

UniProtKB/Swiss-Prot
        BCAT2_HUMAN | O15382: 1ekf 1ekp 1ekv 1kt8 1kta 2a1h 2hdk 2hg8 2hgw 2hgx 2hhf 5bwr 5bwt 5bwu 5bwv 5bwx 5cr5 5hne 5i5s 5i5t 5i5u 5i5v 5i5w 5i5x 5i5y 5i60

(-) Related Entries Specified in the PDB File

5bwr 5bwt 5bwu 5bwv