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(-) Description

Title :  CRYSTAL STRUCTURE OF EVAA, A 2,3-DEHYDRATASE IN COMPLEX WITH DTDP-FUCOSE AND DTDP-RHAMNOSE
 
Authors :  H. M. Holden, R. L. Kubiak, J. B. Thoden
Date :  13 Feb 13  (Deposition) - 22 May 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Nudix Hydrolase Superfamily, Dehydration, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Kubiak, J. B. Thoden, H. M. Holden
Structure Of Evaa: A Paradigm For Sugar 2, 3-Dehydratases.
Biochemistry V. 52 2078 2013
PubMed-ID: 23473392  |  Reference-DOI: 10.1021/BI400176N

(-) Compounds

Molecule 1 - EVAA 2,3-DEHYDRATASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28JT
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EVAA
    Mutation: YES
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Strain: NRRL 18098
    Synonym: PCZA361.3

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11JB2Ligand/Ion[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL] HYDROGEN PHOSPHATE
2TRH2Ligand/Ion2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
11JB2Ligand/Ion[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL] HYDROGEN PHOSPHATE
2TRH2Ligand/Ion2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
11JB2Ligand/Ion[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL] HYDROGEN PHOSPHATE
2TRH2Ligand/Ion2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
11JB2Ligand/Ion[[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(2R,3R,4S,5R,6R)-6-METHYL-3,4,5-TRIS(OXIDANYL)OXAN-2-YL] HYDROGEN PHOSPHATE
2TRH2Ligand/Ion2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:104 , TRP A:106 , GLN A:107 , GLN A:108 , SER A:193 , TRP A:194 , TRP A:288 , TYR A:302 , VAL A:333 , ARG A:351 , GLN A:367 , CYS A:368 , THR A:369 , ASN A:372 , TYR A:373 , HOH A:640 , HOH A:641 , HOH A:642 , HOH A:664 , HOH A:670 , HOH A:696 , HOH A:697 , HOH A:724 , HOH A:852 , HOH A:853 , HOH A:945BINDING SITE FOR RESIDUE TRH A 501
2AC2SOFTWARETRP A:67 , HIS A:78 , PHE A:83 , GLN A:153 , ALA A:154 , THR A:155 , ASN A:158 , TYR A:159 , ASN A:200 , ASN A:238 , TRP A:320 , THR A:321 , GLN A:322 , GLU A:405 , ARG A:408 , HOH A:633 , HOH A:687 , HOH A:689 , HOH A:723 , HOH A:810 , HOH A:811BINDING SITE FOR RESIDUE 1JB A 502
3AC3SOFTWAREARG B:104 , TRP B:106 , GLN B:107 , GLN B:108 , SER B:193 , TRP B:194 , TRP B:288 , TYR B:302 , ARG B:351 , GLN B:367 , CYS B:368 , THR B:369 , ASN B:372 , TYR B:373 , HOH B:648 , HOH B:649 , HOH B:663 , HOH B:664 , HOH B:667 , HOH B:669 , HOH B:708 , HOH B:818 , HOH B:819 , HOH B:850BINDING SITE FOR RESIDUE TRH B 501
4AC4SOFTWARETRP B:67 , PHE B:83 , GLY B:117 , GLN B:153 , ALA B:154 , THR B:155 , ASN B:158 , TYR B:159 , ASN B:200 , ASN B:238 , TRP B:320 , THR B:321 , GLN B:322 , GLU B:405 , ARG B:408 , HOH B:630 , HOH B:695 , HOH B:760 , HOH B:778 , HOH B:802 , HOH B:826 , HOH B:829BINDING SITE FOR RESIDUE 1JB B 502

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:286 -B:286

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:101 -Pro A:102
2Ala A:175 -Pro A:176
3Gly B:101 -Pro B:102
4Ala B:175 -Pro B:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J7G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J7G)

(-) Exons   (0, 0)

(no "Exon" information available for 4J7G)

(-) 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:448
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeeeehhhhh..eee......eee......eeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeeeeee..eeeeeeeeee.......eeee..eeehhhhh....hhhhhh..hhh.eeeeeeee.........eeeeeeee..........eeeeehhhhhhhh......hhhhhhhhh.............hhhhhhhhhhhhhhh.eeeeeeehhhhh..eee....eee.....eeeeeeeee...eeeeeeeee...eeeeeeeeee..eeeeeeeee.........eee..eeehhhhhh..hhhhh..hhhhhhh.hhh.eeeeeeee.........eeeeeeee..........eeeehhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7g A  11 AVRPRDHHDYADRIALSAATTDGVQMRTEDVRAWIAERRDANVFHVERIPFADLDQWWFEGVTGNLVHRSGRFFTIEGLHVIEHDGPHGDGPYREWQQPVIRQPEVGILGILAKEFDGVLHFLMQAKMEPGNPNLVQLSPTVQATRSNYTNVKLIEYFAPPDPERVIVDVLQAEQGSWFFRKSNRNMIVETVDDVPLWDDFCWLTLGQIAELMHEDETINMNSRSVLSCLPYQDITPRALFSDVQLLSWFTNERSRHDVRVRRIPLADVCGWKQGAEEIEHEDGRYFKVLAVAVKGSISWTQPLVESVDLGVVAFLVRKIDGVPHVLVQARVDGGFLDTVELAPTVQCTPLNYAHLPAEEAPPFLDLVQNAPRSRIRYEAIHSEEGGRFLGVRARYLVIDADEAIDPPPGYAWVTPAQLTALTRHGHYVNVEARTLLACINAAAAQPR 468
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      176       186       196       206       216       226       236       246       256       266       276       286       296       306      |320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
                                                                                                                                                                               160|                                                                                                                                               313|                                                                                                                                                      
                                                                                                                                                                                167                                                                                                                                                318                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhh........hhhhhhhhhhhhh...eeeeehhhhh..eee......eee......eeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeeeeee..eeeeeeeeee.......eeee..eeehhhhh...hhhhhh..hhh.eeeeeeee.........eeeeeeee..........eeeeehhhhhhhh......hhhhhhhhh.............hhhhhhhhhhhhhhh.eeeeeeehhhhh..eee....eee.....eeeeeeeee...eeeeeeee...eeeeeeeeee..eeeeeeeee.........eee..eeehhhhhh..hhhhh..hhhhhhh.hhh.eeeeeeee.........eeeeeeee..........eeeehhhhhhhhh......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7g B  11 AVRPRDHHDYADRIALSAATTDGVQMRTEDVRAWIAERRDANVFHVERIPFADLDQWWFEGVTGNLVHRSGRFFTIEGLHVIEHDGPHGDGPYREWQQPVIRQPEVGILGILAKEFDGVLHFLMQAKMEPGNPNLVQLSPTVQATRSNYNVKLIEYFAPPDPERVIVDVLQAEQGSWFFRKSNRNMIVETVDDVPLWDDFCWLTLGQIAELMHEDETINMNSRSVLSCLPYQDITPRALFSDVQLLSWFTNERSRHDVRVRRIPLADVCGWKQGAEEIEHEDGRYFKVLAVAVKGISWTQPLVESVDLGVVAFLVRKIDGVPHVLVQARVDGGFLDTVELAPTVQCTPLNYAHLPAEEAPPFLDLVQNAPRSRIRYEAIHSEEGGRFLGVRARYLVIDADEAIDPPPGYAWVTPAQLTALTRHGHYVNVEARTLLACINAAAAQPR 468
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307    || 322       332       342       352       362       372       382       392       402       412       422       432       442       452       462      
                                                                                                                                                                              159|                                                                                                                                              312|                                                                                                                                                      
                                                                                                                                                                               167                                                                                                                                               318
   Legend:   → Mismatch (orange background)
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  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 4J7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J7G)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4J7G)

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        O52793_AMYOR | O52793: 4j7h

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4j7h