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(-) Description

Title :  CRYSTAL STRUCTURE OF GH3.12 IN COMPLEX WITH AMP AND SALICYLATE
 
Authors :  C. Westfall, C. Zubieta, M. Nanao, J. Herrmann, J. Jez
Date :  19 Apr 12  (Deposition) - 20 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Firefly Luciferase Family, Acyl Adenylase, Amino Acid Conjugation, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Westfall, C. Zubieta, J. Herrmann, U. Kapp, M. H. Nanao, J. M. Jez
Structural Basis For Prereceptor Modulation Of Plant Hormones By Gh3 Proteins.
Science V. 336 1708 2012
PubMed-ID: 22628555  |  Reference-DOI: 10.1126/SCIENCE.1221863

(-) Compounds

Molecule 1 - 4-SUBSTITUTED BENZOATES-GLUTAMATE LIGASE GH3.12
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GH3.12, GDG1, PBS3, WIN3, AT5G13320, T22N19.5, T31B5.140
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: AUXIN-RESPONSIVE GH3-LIKE PROTEIN 12, ATGH3-12, PROTEIN GH3- LIKE DEFENSE GENE 1, PROTEIN GRETCHEN HAGEN 3.12, PROTEIN HOPW1-1- INTERACTING 3, PROTEIN AVRPPHB SUSCEPTIBLE 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2SAL2Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2SAL2Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:95 , SER A:96 , VAL A:299 , THR A:301 , THR A:324 , TYR A:325 , GLY A:326 , SER A:327 , SER A:328 , TYR A:347 , ASP A:398 , PHE A:414 , ARG A:417 , LYS A:428 , SAL A:602 , HOH A:764 , HOH A:1267BINDING SITE FOR RESIDUE AMP A 601
2AC2SOFTWARETYR A:120 , ARG A:123 , THR A:161 , ILE A:217 , THR A:324 , GLY A:326 , AMP A:601 , HOH A:737 , HOH A:1066 , HOH A:1132BINDING SITE FOR RESIDUE SAL A 602
3AC3SOFTWARESER B:95 , SER B:96 , VAL B:299 , THR B:301 , THR B:324 , TYR B:325 , GLY B:326 , SER B:327 , SER B:328 , TYR B:347 , ASP B:398 , PHE B:414 , ARG B:417 , SAL B:602 , HOH B:864 , HOH B:886 , HOH B:1266BINDING SITE FOR RESIDUE AMP B 601
4AC4SOFTWARELEU B:116 , TYR B:120 , ARG B:123 , THR B:161 , ILE B:217 , THR B:324 , GLY B:326 , AMP B:601 , HOH B:716 , HOH B:1033 , HOH B:1042BINDING SITE FOR RESIDUE SAL B 602

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:464 -Pro A:465
2Phe B:464 -Pro B:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EQL)

(-) 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:494
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhh..hhhhh......eeeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhh......eeee.......ee.....eeehhhhhhhhhhhhhh...hhhhh...hhhhhhh.hhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhh....eeeee.hhhhhhhhhhhhhhhh...ee..eee....eeee......hhhhh.eee.....eeeeee.........ee.hhh....eeeeeee.......ee..eeeeeeeee..eeeeeeeee..eee......eehhhhhhhhhhh.eeee......eeeee...hhhhhhhhhhhhhhh.hhhhhhhhhh.......eee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eql A   8 NETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSSGTSGGAQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEEGKGMMFLFTKQESMTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIPMDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQATSYADTSTFPGHYVVYLELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRVKFFS 574
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   ||  461       471||     496       506       516       526|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                           441|             472|                                   526|   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            456              488                                    571   


Chain B from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhh..hhhhh......eeeeeeee....eeeeeehhhhhhhhhhhhhhhhhhhhhhh......eeee.......ee.....eeehhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhh....eeeee.hhhhhhhhhhhhhhhh...ee..eee....eeee......hhhhh.eee.....eeeeee.........ee.hhh....eeeeeee.......ee..eeeeeeeee..eeeeeeeee..eee......ee...eeee......eeeee..hhhhhhhhhhhhhhhhhhhhh.......eee..ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eql B   9 ETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSSGTSGGAQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEEGKGMMFLFTKQESMTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIPMDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEETSYADTSTFPGHYVVYLLSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRAKFFSI 575
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428   ||  461       471||     502       512       522  ||     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 432|             472|                            525|     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  456              494                             570
   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 4EQL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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        GH312_ARATH | Q9LYU4: 4epm 4eq4 4ewv 4l39

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4epl 4epm 4eq4 4ewv