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(-) Description

Title :  CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH 2-FLUORO BENZOIC ACID
 
Authors :  S. Strom, M. Nosrati, C. Thornburg, K. D. Walker, J. H. Geiger
Date :  18 Oct 14  (Deposition) - 30 Sep 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.77
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Substrate Specificity, Kinetics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. K. Thornburg, S. Wortas-Strom, M. Nosrati, J. H. Geiger, K. D. Walke
Kinetically And Crystallographically Guided Mutations Of A Benzoate Coa Ligase (Bada) Elucidate Mechanism And Expand Substrate Permissivity.
Biochemistry V. 54 6230 2015
PubMed-ID: 26378464  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00899

(-) Compounds

Molecule 1 - BENZOATE-COENZYME A LIGASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BADA
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076

 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  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
13U43Ligand/Ion2-FLUOROBENZOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
13U42Ligand/Ion2-FLUOROBENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13U41Ligand/Ion2-FLUOROBENZOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:227 , TYR A:228 , ALA A:302 , GLY A:303 , ILE A:326 , GLY A:327 , SER A:328 , LEU A:332 , LYS A:427 , HOH A:1123 , HOH A:1185BINDING SITE FOR RESIDUE 3U4 A 1000
2AC2SOFTWAREALA A:221 , PHE A:272 , GLY A:274 , ALA A:275 , GLY A:278 , MET A:282 , HOH A:1398 , HOH A:1438BINDING SITE FOR RESIDUE 3U4 A 1001
3AC3SOFTWAREALA B:227 , TYR B:228 , ALA B:302 , GLY B:303 , ILE B:326 , GLY B:327 , SER B:328 , LEU B:332 , HIS B:333 , LYS B:427 , HOH B:1168 , HOH B:1247BINDING SITE FOR RESIDUE 3U4 B 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RM2)

(-) Exons   (0, 0)

(no "Exon" information available for 4RM2)

(-) 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:516
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhh......eeee....eeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.....eeeee..........eehhhhhhh..............eeeeeee.......eeeeeehhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhh.........eeeehhhhhhhhhh.....hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee......eeee............ee....eeeee...........eeeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhh..eeee............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rm2 A   6 VTPPPEKFNFAEHLLQTNRVRPDKTAFVDDISSLSFAQLEAQTRQLAAALRAIGVKREERVLLLMLDGTDWPVAFLGAIYAGIVPVAVNTLLTADDYAYMLEHSRAQAVLVSGALHPVLKAALTKSDHEVQRVIVSRPAAPLEPGEVDFAEFVGAHAPLEKPAATQADDPAFWLYSSGSTGRPKGVVHTHANPYWTSELYGRNTLHLREDDVCFSAAKLFFAYGLGNALTFPMTVGATTLLMGERPTPDAVFKRWLGGVGGVKPTVFYGAPTGYAGMLAAPNLPSRDQVALRLASSAGEALPAEIGQRFQRHFGLDIVDGIGSTEMLHIFLSNLPDRVRYGTTGWPVPGYQIELRGDGGGPVADGEPGDLYIHGPSSATMYWGNRAKSRDTFQGGWTKSGDKYVRNDDGSYTYAGRTDDMLKVSGIYVSPFEIEATLVQHPGVLEAAVVGVADEHGLTKPKAYVVPRPGQTLSETELKTFIKDRLAPYKYPRSTVFVAELPKTATGKIQRFKLREG 521
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515      


Chain B from PDB  Type:PROTEIN  Length:519
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh......eeee....eeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh.....eeeee.........eeehhhhhhh..............eeeeeee.......eeeeeehhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhh.........eeeehhhhhhhhhhh....hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee......eeee............ee....eeeee...........eeeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhh...hhhhh..eeee............hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rm2 B   6 VTPPPEKFNFAEHLLQTNRVRPDKTAFVDDISSLSFAQLEAQTRQLAAALRAIGVKREERVLLLMLDGTDWPVAFLGAIYAGIVPVAVNTLLTADDYAYMLEHSRAQAVLVSGALHPVLKAALTKSDHEVQRVIVSRPAAPLEPGEVDFAEFVGAHAPLEKPAATQADDPAFWLYSSGSTGRPKGVVHTHANPYWTSELYGRNTLHLREDDVCFSAAKLFFAYGLGNALTFPMTVGATTLLMGERPTPDAVFKRWLGGVGGVKPTVFYGAPTGYAGMLAAPNLPSRDQVALRLASSAGEALPAEIGQRFQRHFGLDIVDGIGSTEMLHIFLSNLPDRVRYGTTGWPVPGYQIELRGDGGGPVADGEPGDLYIHGPSSATMYWGNRAKSRDTFQGGWTKSGDKYVRNDDGSYTYAGRTDDMLKVSGIYVSPFEIEATLVQHPGVLEAAVVGVADEHGLTKPKAYVVPRPGQTLSETELKTFIKDRLAPYKYPRSTVFVAELPKTATGKIQRFKLREGVLG 524
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515
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  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 4RM2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RM2)

(-) Gene Ontology  (5, 5)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q93TK0_RHOPL | Q93TK0: 4rmn 4zjz
UniProtKB/TrEMBL
        Q93TK0_RHOPL | Q93TK0: 4eat 4rlf 4rlq 4rm3

(-) Related Entries Specified in the PDB File

2v7b 4eat 4rlf 4rlq