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(-) Description

Title :  CRYSTAL STRUCTURE OF A BENZOATE COENZYME A LIGASE
 
Authors :  J. Geiger, S. Strom
Date :  22 Mar 12  (Deposition) - 27 Mar 13  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  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
    EC Number: 6.2.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    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  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1BEZ2Ligand/IonBENZOIC ACID
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1BEZ1Ligand/IonBENZOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:227 , TYR A:228 , GLY A:303 , ILE A:326 , GLY A:327 , SER A:328 , LEU A:332 , HIS A:333 , HOH A:1340BINDING SITE FOR RESIDUE BEZ A 1000
2AC2SOFTWAREPHE A:13 , ASN A:14 , HOH A:1247BINDING SITE FOR RESIDUE EDO 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:1202 , HOH B:1213BINDING SITE FOR RESIDUE BEZ B 1000
4AC4SOFTWARETHR A:129 , LYS A:130 , SER B:182 , GLY B:183 , GLY B:186 , ARG B:187 , PRO B:188 , SER B:434 , HOH B:1167 , HOH B:1293BINDING SITE FOR RESIDUE GOL B 1001
5AC5SOFTWARELEU B:71 , THR B:95 , LEU B:96 , GLY B:248 , HOH B:1280BINDING SITE FOR RESIDUE GOL B 1002
6AC6SOFTWARELYS A:125 , GLU A:148 , HOH A:1164 , HOH A:1423 , GLU B:439 , VAL B:443 , GLU B:450 , ALA B:451 , HOH B:1204 , HOH B:1409BINDING SITE FOR RESIDUE GOL B 1003
7AC7SOFTWAREGLU B:358 , LEU B:359 , ARG B:410 , HOH B:1193 , HOH B:1229BINDING SITE FOR RESIDUE EDO B 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EAT)

(-) 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 d4eata_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh......eeee....eeehhhhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh...eeee..hhhhhhhhhhhh......eeee.........eeehhhhhhh..............eeeeeee.......eeeeeehhhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhh.........eeeehhhhhhhhhhh....hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee......eeee............ee....eeeee...........eeeeeee..........hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhh..hhhhh..eeee............hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eat 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 d4eatb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            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.......eeeeee.hhhhhhhhhh...........eeee.....hhhhhhhhhhhhhhhh.eee......hhhhhhhhhh.........eeeehhhhhhhhhhh....hhhhh...eeee.....hhhhhhhhhhhhh..eeeeee......eeee............ee....eeeee............eeeeee......ee..hhhhhhhhee..eeeeeeeeee.....eeeeee....eee..eeehhhhhhhhhh....eeeeeeeeee.....eeeeeeeee......hhhhhhhhhhh..hhhhh..eeee............hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eat 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)
  - → 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  (1, 2)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  4eat
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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: 4rmn 4zjz
UniProtKB/TrEMBL
        Q93TK0_RHOPL | Q93TK0: 4rlf 4rlq 4rm2 4rm3

(-) Related Entries Specified in the PDB File

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