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(-) Description

Title :  CRYSTAL STRUCTURE OF SELENO-METHIONINE DERIVATIZED GH3.12
 
Authors :  C. Zubieta, M. Nanao, J. Jez, C. Westfall, U. Kapp
Date :  18 Apr 12  (Deposition) - 20 Jun 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
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  (3, 33)

Asymmetric Unit (3, 33)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MSE29Mod. Amino AcidSELENOMETHIONINE
3SAL2Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 1 (3, 17)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MSE15Mod. Amino AcidSELENOMETHIONINE
3SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 2 (3, 16)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MSE14Mod. Amino AcidSELENOMETHIONINE
3SAL1Ligand/Ion2-HYDROXYBENZOIC ACID
Biological Unit 3 (3, 33)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MSE29Mod. Amino AcidSELENOMETHIONINE
3SAL2Ligand/Ion2-HYDROXYBENZOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:116 , TYR A:120 , ARG A:123 , THR A:161 , ILE A:217 , THR A:324 , GLY A:326 , HOH A:831 , HOH A:973BINDING SITE FOR RESIDUE SAL A 601
2AC2SOFTWARESER 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 , HOH A:802BINDING SITE FOR RESIDUE AMP A 602
3AC3SOFTWARELEU B:116 , TYR B:120 , ARG B:123 , ILE B:217 , THR B:324 , HOH B:719 , HOH B:814BINDING SITE FOR RESIDUE SAL B 601
4AC4SOFTWARESER 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 , HOH B:789BINDING SITE FOR RESIDUE AMP B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EQ4)

(-) 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 4EQ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EQ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4EQ4)

(-) 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:545
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhh..hhhhh......eeeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhhhh......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......eehhhhhhhhhhhhhhhhhh..eeeeee......eeeeee......hhhhhhhhhhhhh.hhhhhhhhhh.......eeeee.......................hhhhhhhhhh.eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eq4 A   8 NETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSSGTSGGAQKmmPWNNKYLDNLTFIYDLRmQVITKHVKGVEEGKGmmFLFTKQESmTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVmVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSmGQYVPmLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFmPNmSYFEFIPmDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRmRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGDFTSYADTSTFPGHYVVYLEVELDEEALSTCCLVmEESLDNVYKRCRFKDGSIGPLEIRVVRQGTFDSLmDFFISQYKTPRCIKSGKALQVLETCVVAKFFSI 575
                                    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       447 ||    461       471  ||   494      |504       514       524       534 |     550       560       570     
                                                                                                                           105-MSE            124-MSE         140-MSE   150-MSE                                                                 222-MSE                                                                           304-MSE |                                     350-MSE    361-MSE                          394-MSE                                                449|                 474|          501-MSE                            536-MSE42|                          
                                                                                                                            106-MSE                            141-MSE                                                                                                                                                                  310-MSE                                    353-MSE                                                                                          454                  488                                                    549                          


Chain B from PDB  Type:PROTEIN  Length:531
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhh.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......eehhhhhhhhhhhhhhhhhhh.........ee......ee..........hhhhhhhhhhhhhhh.hhhhhhhhhh........eee.......hhhhhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eq4 B   9 ETFEKQLKDLTSNVKSIQDNLLEEIITPNTKTEYLQRFLIDRFDKELFKKNVPIVSYEDIKPYLDRVVNGESSDVISARTITGFLLSSGTSGGAQKmmPWNNKYLDNLTFIYDLRmQVITKHVKGVEEGKGmmFLFTKQESmTPSGLPARVATSSYFKSDYFKNRPSNWYYSYTSPDEVILCPNNTESLYCHLLCGLVQRDEVVRTGSIFASVmVRAIEVLKNSWEELCSNIRSGHLSNWVTDLGCQNSVSLVLGGPRPELADTIEEICNQNSWKGIVKRLWPNTKYIETVVTGSmGQYVPmLNYYCNDLPLVSTTYGSSETTFGINLDPLCKPEDVSYTFmPNmSYFEFIPmDGGDKNDVVDLEDVKLGCTYEPVVTNFAGLYRmRVGDIVLVTGFYNNAPQFKFVRRENVVLSIDSDKTNEEDLFKAVSQAKLVLESSGLDLKDFTSYADTSTFPGHYVVYLEVDTELDEEALSTCCLVmEESLDNVYKRCRFKDGSIGPLEIRVVTPRCIKSGKALQVLETCVVAKFF 573
                                    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       438       448       458       468       489       499 |     509       519       552       562       572 
                                                                                                                          105-MSE            124-MSE         140-MSE   150-MSE                                                                 222-MSE                                                                           304-MSE |                                     350-MSE    361-MSE                          394-MSE                                                                           476|          501-MSE                   527|                      
                                                                                                                           106-MSE                            141-MSE                                                                                                                                                                  310-MSE                                    353-MSE                                                                                                                     488                                     551
   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 4EQ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EQ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EQ4)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        GH312_ARATH | Q9LYU4: 4epm 4eql 4ewv 4l39

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