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(-) Description

Title :  CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE WITH 2-THIOPHENE CARBOXYLIC ACID
 
Authors :  S. Strom, M. Nosrati, C. Thornburg, K. D. Walker, J. H. Geiger
Date :  21 Oct 14  (Deposition) - 30 Sep 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  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 (1x)B (1x)
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1C214Ligand/IonTHIOPHENE-2-CARBOXYLIC ACID
2GOL7Ligand/IonGLYCEROL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1C212Ligand/IonTHIOPHENE-2-CARBOXYLIC ACID
2GOL6Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1C212Ligand/IonTHIOPHENE-2-CARBOXYLIC ACID
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1C212Ligand/IonTHIOPHENE-2-CARBOXYLIC ACID
2GOL6Ligand/IonGLYCEROL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:228 , ALA A:302 , GLY A:303 , GLY A:327 , SER A:328 , LEU A:332 , HIS A:333 , ILE A:334 , LYS A:427 , HOH A:1235 , HOH A:1357BINDING SITE FOR RESIDUE C21 A 1000
02AC2SOFTWAREALA A:221 , ALA A:222 , PHE A:226 , TYR A:228 , GLY A:274 , ALA A:275 , ALA A:302 , GLY A:303 , GLY A:430 , HOH A:1189 , HOH A:1235 , HOH A:1356BINDING SITE FOR RESIDUE C21 A 1001
03AC3SOFTWAREALA A:305 , LEU A:306 , ASP A:324 , GLY A:346 , THR A:347 , THR A:348 , THR A:417 , TYR A:418BINDING SITE FOR RESIDUE GOL A 1002
04AC4SOFTWARETYR B:228 , ALA B:302 , GLY B:303 , GLY B:327 , SER B:328 , LEU B:332 , HIS B:333 , ILE B:334 , LYS B:427 , HOH B:1227 , HOH B:1350BINDING SITE FOR RESIDUE C21 B 1000
05AC5SOFTWAREALA B:222 , PHE B:226 , TYR B:228 , GLY B:274 , ALA B:275 , ALA B:302 , GLY B:303 , GLY B:430 , HOH B:1158 , HOH B:1227 , HOH B:1288 , HOH B:1331BINDING SITE FOR RESIDUE C21 B 1001
06AC6SOFTWARETHR A:129 , LYS A:130 , SER B:182 , GLY B:183 , SER B:184 , GLY B:186 , ARG B:187 , PRO B:188 , SER B:434 , GLU B:437 , HOH B:1123 , HOH B:1333BINDING SITE FOR RESIDUE GOL B 1002
07AC7SOFTWARELEU B:71 , THR B:95 , LEU B:96 , LYS B:223 , GLY B:248 , HOH B:1206 , HOH B:1207 , HOH B:1355BINDING SITE FOR RESIDUE GOL B 1003
08AC8SOFTWAREASP B:101 , SER B:182 , PRO B:188 , GLU B:437 , LYS B:494 , HOH B:1176 , HOH B:1361BINDING SITE FOR RESIDUE GOL B 1004
09AC9SOFTWAREILE B:357 , GLU B:358 , LEU B:359 , ARG B:410 , TYR B:416 , HOH B:1225 , HOH B:1347 , HOH B:1368BINDING SITE FOR RESIDUE GOL B 1005
10BC1SOFTWAREASP B:75 , VAL B:140 , SER B:141 , ARG B:142 , PRO B:143 , ASP B:153 , PHE B:154 , ALA B:155 , HOH B:1344BINDING SITE FOR RESIDUE GOL B 1006
11BC2SOFTWAREPHE B:13 , ASN B:14 , GLU B:17 , HIS B:18BINDING SITE FOR RESIDUE GOL B 1007

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RMN)

(-) 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:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               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............eeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhhhhhhhhh..eeee............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rmn A   6 VTPPPEKFNFAEHLLQTNRVRPDKTAFVDDISSLSFAQLEAQTRQLAAALRAIGVKREERVLLLMLDGTDWPVAFLGAIYAGIVPVAVNTLLTADDYAYMLEHSRAQAVLVSGALHPVLKAALTKSDHEVQRVIVSRPAAPLEPGEVDFAEFVGAHAPLEKPAATQADDPAFWLYSSGSTGRPKGVVHTHANPYWTSELYGRNTLHLREDDVCFSAAKLFFAYGLGNALTFPMTVGATTLLMGERPTPDAVFKRWLGGVGGVKPTVFYGAPTGYAGMLAAPNLPSRDQVALRLASSAGEALPAEIGQRFQRHFGLDIVDGIGSTEMLHIFLSNLPDRVRYGTTGWPVPGYQIELRGDGGGPVADGEPGDLYIHGPSSATMYWGNRAKSRDTFQGGWTKSGDKYVRNDDGSYTYAGRTDDMLKVSGIYVSPFEIEATLVQHPGVLEAAVVGVADEHGLTKPKAYVVPRPGQTLSETELKTFIKDRLAPYKYPRSTVFVAELPKTATGKIQRFKLREGVL 523
                                    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............eeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhh..hhhhh..eeee............hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rmn 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
   Legend:   → Mismatch (orange background)
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    → 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 4RMN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 11)

Asymmetric Unit(hide GO term definitions)

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  Q93TK0_RHOPL | Q93TK0
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q93TK0_RHOPL | Q93TK0: 4zjz
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        Q6NC13_RHOPA | Q6NC13: 4zjz
        Q93TK0_RHOPL | Q93TK0: 4eat 4rlf 4rlq 4rm2 4rm3

(-) Related Entries Specified in the PDB File

2v7b 4eat 4rlf 4rlq 4rm3