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(-) Description

Title :  CRYSTAL STRUCTURE OF GH3.12 FROM ARABIDOPSIS THALIANA IN COMPLEX WITH AMPCPP AND SALICYLATE
 
Authors :  C. Zubieta, J. M. Jez, E. Brown, R. Marcellin, U. Kapp, A. Round, C. Westf
Date :  05 Jun 13  (Deposition) - 02 Oct 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Acyl Acid Amido Synthase, Protein-Ligand Complex, Magnesium, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Round, E. Brown, R. Marcellin, U. Kapp, C. S. Westfall, J. M. Jez, C. Zubieta
Determination Of The Gh3. 12 Protein Conformation Through Hplc-Integrated Saxs Measurements Combined With X-Ray Crystallography.
Acta Crystallogr. , Sect. D V. 69 2072 2013
PubMed-ID: 24100325  |  Reference-DOI: 10.1107/S0907444913019276

(-) 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
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: GH3.12 ACYL ACID AMIDO SYNTHETASE, 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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1APC2Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG1Ligand/IonMAGNESIUM ION
3SAL2Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1APC1Ligand/IonDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
2MG-1Ligand/IonMAGNESIUM ION
3SAL1Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:329 , VAL A:396 , APC A:603BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWARELEU A:116 , TYR A:120 , ARG A:123 , THR A:324 , GLY A:326BINDING SITE FOR RESIDUE SAL A 602
3AC3SOFTWARESER A:95 , VAL A:299 , THR A:301 , THR A:324 , GLY A:326 , SER A:327 , SER A:328 , TYR A:347 , ASP A:398 , PHE A:414 , MG A:601 , HOH A:755 , HOH A:766BINDING SITE FOR RESIDUE APC A 603
4AC4SOFTWARETYR B:120 , ARG B:123 , ILE B:217 , THR B:324 , APC B:602BINDING SITE FOR RESIDUE SAL B 601
5AC5SOFTWARESER B:95 , SER B:96 , LYS B:104 , THR B:301 , THR B:324 , TYR B:325 , GLY B:326 , SER B:327 , SER B:328 , TYR B:347 , ASP B:398 , LYS B:428 , SAL B:601 , HOH B:755 , HOH B:765BINDING SITE FOR RESIDUE APC B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L39)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Phe A:464 -Pro A:465
2Ser B:95 -Ser B:96
3Phe B:464 -Pro B:465

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L39)

(-) Exons   (0, 0)

(no "Exon" information available for 4L39)

(-) 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:541
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhh..hhhhh......eeee....eeee.hhhhhhhhhhhhhhhhhhhhhh......eeee.......ee.....eeeehhhhhhhhhhhhh...hhhhh...hhhhhhh.hhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhh....eeeee.hhhhhhhhhhhhhhhh...ee..eee....eeee......hhhhh.eee.....eeeeee.........ee.hhh....eeeeeee.......ee..eeeeeeeee..eeeeeeeee............hhhhhhhhhh.hhhhhhh.........eeee......eeee.............hhhhhhhhhh..hhhhhhhhh........ee.........hhhhhh..........hhhhhhhh....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l39 A   9 ETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSAQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEEGKGMMFLFTKQESMTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIPMDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGLDLKDFTSYADTSTFPGHYVVYLEGEQFELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRVVGTFDSLMDFFISQGQYKTPRCKALQVLETCVVAKFFSI 575
                                    18        28        38        48        58        68        78        88      |104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       479||     494       504       514       524  ||   536      |550   ||  564       574 
                                                                                                                 95|                                                                                                                                                                                                                                                                                                                                                                                473|||                                      527|          543|   554|                
                                                                                                                 102                                                                                                                                                                                                                                                                                                                                                                                 479||                                       530           548    559                
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      480|                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       486                                                                               


Chain B from PDB  Type:PROTEIN  Length:542
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh...hhhhhhhhhhhhhh..hhhhh......eeeee...eeeee.hhhhhhhhhhhhhhhhhhhhhh.hhhhheeee.......ee.....eeehhhhhhhhhhhhhh...hhhhh...hhhhhh..hhhhhhhhhhhhhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.....hhhhhhh.....eeee.hhhhhhhhhhhhhhhh...ee..eee....eeee......hhhhh.eee.....eeeeee.........ee.hhh....eeeeeee.......ee..eeeeeeeee..eeeeeeeee..............hhhhhhhh.........................eeee.....hhhhhh..........hhhhhhhhhh.......eeee.........hhhhhh.............hhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l39 B   8 NETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSSAQKMMPWNNKYLDNLTFIYDLRMQVITKHVKGVEEGKGMMFLFTKQESMTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVMVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSMGQYVPMLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFMPNMSYFEFIPMDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRMRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSKDFTSYADTSTFPGHYVVYLEQFELDEEALSTCCLVMEESLDNVYKRCRFKDGSIGPLEIRVVRQGTFDSLMDFFISTGQYKTPRCIKSGKALQVLETCVVAKFFS 574
                                    17        27        37        47        57        67        77        87       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442     ||456       466      |488       498       508       518       528       538  ||   552       562       572  
                                                                                                                   96|                                                                                                                                                                                                                                                                                                                                                       448|                 473|                                                    541|                            
                                                                                                                   102                                                                                                                                                                                                                                                                                                                                                        453                  486                                                     546
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4L39)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L39)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4l39
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  6.3.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        GH312_ARATH | Q9LYU4: 4epm 4eq4 4eql 4ewv

(-) Related Entries Specified in the PDB File

4epm 4eq4 4eql 4ewv