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(-) Description

Title :  GLYCEROL TRINITRATE REDUCTASE NERA FROM AGROBACTERIUM RADIOBACTER
 
Authors :  G. Oberdorfer, K. Gruber
Date :  05 Mar 13  (Deposition) - 08 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Tim-Barrel, Ene-Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Oberdorfer, A. Binter, S. Wallner, K. Durchschein, M. Hall, K. Faber, P. Macheroux, K. Gruber
The Structure Of Glycerol Trinitrate Reductase Nera From Agrobacterium Radiobacter Reveals The Molecular Reason For Nitro- And Ene-Reductase Activity In Oye Homologues.
Chembiochem V. 14 836 2013
PubMed-ID: 23606302  |  Reference-DOI: 10.1002/CBIC.201300136

(-) Compounds

Molecule 1 - GTN REDUCTASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NERA
    Organism Common: AGROBACTERIUM TUMEFACIENS
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1FMN3Ligand/IonFLAVIN MONONUCLEOTIDE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
3SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:22 , PRO A:23 , LEU A:24 , THR A:25 , GLY A:55 , GLN A:97 , HIS A:178 , ASN A:181 , ARG A:230 , THR A:271 , ASN A:305 , ASN A:306 , GLY A:307 , PHE A:327 , GLY A:328 , LYS A:329 , PHE A:355 , TYR A:356 , PEG A:402 , HOH A:554 , HOH A:555 , HOH A:610 , HOH A:736 , HOH A:747BINDING SITE FOR RESIDUE FMN A 401
2AC2SOFTWAREHIS A:178 , ASN A:181 , TYR A:183 , THR A:271 , FMN A:401 , HOH A:517 , HOH A:533 , HOH A:747 , HOH A:1068 , HOH A:1102 , HOH A:1104BINDING SITE FOR RESIDUE PEG A 402
3AC3SOFTWAREARG A:339 , ASN A:343 , HOH A:1130BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWAREALA B:22 , PRO B:23 , LEU B:24 , THR B:25 , GLY B:55 , GLN B:97 , HIS B:178 , ASN B:181 , ARG B:230 , ASN B:305 , ASN B:306 , GLY B:307 , PHE B:327 , GLY B:328 , LYS B:329 , PHE B:355 , TYR B:356 , HOH B:519 , HOH B:536 , HOH B:600 , HOH B:656 , HOH B:679 , HOH B:1101BINDING SITE FOR RESIDUE FMN B 401
5AC5SOFTWAREARG B:339 , ASN B:343BINDING SITE FOR RESIDUE SO4 B 402
6AC6SOFTWAREALA C:22 , PRO C:23 , LEU C:24 , THR C:25 , GLY C:55 , GLN C:97 , HIS C:178 , ASN C:181 , ARG C:230 , THR C:271 , ASN C:305 , ASN C:306 , GLY C:307 , PHE C:327 , GLY C:328 , LYS C:329 , TYR C:356 , HOH C:521 , HOH C:560 , HOH C:647 , HOH C:664 , HOH C:732BINDING SITE FOR RESIDUE FMN C 401
7AC7SOFTWAREARG C:339 , ASN C:343BINDING SITE FOR RESIDUE SO4 C 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:135 -Thr A:136
2Ala A:138 -Phe A:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JIC)

(-) 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:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jica_ A: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee.......hhhhh.hhhhhhhhhh.....eeeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh..ee........ee...........ee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhh.....eeeee.................hhhhhhhhhhhh....eeeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jic A   2 TSLFEPAQAGDIALANRIVMAPLTRNRSPGAIPNNLNATYYEQRATAGLIVTEGTPISQQGQGYADVPGLYKREAIEGWKKITDGVHSAGGKIVAQIWHVGRISHTSLQPHGGQPVAPSAITAKSKTYIINDDGTGAFAETSEPRALTIDDIGLILEDYRSGARAALEAGFDGVEIHAANGYLIEQFLKSSTNQRTDDYGGSIENRARFLLEVVDAVAEEIGAGRTGIRLSPVTPANDIFEADPQPLYNYVVEQLGKRNLAFIHVVEGATGGPRDFKQGDKPFDYASFKAAYRNAGGKGLWIANNGYDRQSAIEAVESGKVDAVAFGKAFIANPDLVRRLKNDAPLNAPNQPTFYGGGAEGYTDYPALAQ 371
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371


Chain B from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jicb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee.......hhhhh.hhhhhhhhhh.....eeeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh..ee........eeeee.....eeeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhh.....eeeee.................hhhhhhhhhhhh....eeeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhhh......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jic B   2 TSLFEPAQAGDIALANRIVMAPLTRNRSPGAIPNNLNATYYEQRATAGLIVTEGTPISQQGQGYADVPGLYKREAIEGWKKITDGVHSAGGKIVAQIWHVGRISHTSLQPHGGQPVAPSAITAKSKTYIINDDGTGAFAETSEPRALTIDDIGLILEDYRSGARAALEAGFDGVEIHAANGYLIEQFLKSSTNQRTDDYGGSIENRARFLLEVVDAVAEEIGAGRTGIRLSPVTPANDIFEADPQPLYNYVVEQLGKRNLAFIHVVEGATGGPRDFKQGDKPFDYASFKAAYRNAGGKGLWIANNGYDRQSAIEAVESGKVDAVAFGKAFIANPDLVRRLKNDAPLNAPNQPTFYGGGAEGYTDYPALAQ 371
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371


Chain C from PDB  Type:PROTEIN  Length:370
                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jicc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee...eee.......hhhhh.hhhhhhhhhh.....eeeeeeee...............hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhh..ee........eeeee.....eeeee....ee.hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhh...hhhhhhhhhhhhhh.....eeeee.................hhhhhhhhhhhh....eeeee...hhhhhhhhhhh....eeeehhhhhhh.hhhhhhhh.......hhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jic C   2 TSLFEPAQAGDIALANRIVMAPLTRNRSPGAIPNNLNATYYEQRATAGLIVTEGTPISQQGQGYADVPGLYKREAIEGWKKITDGVHSAGGKIVAQIWHVGRISHTSLQPHGGQPVAPSAITAKSKTYIINDDGTGAFAETSEPRALTIDDIGLILEDYRSGARAALEAGFDGVEIHAANGYLIEQFLKSSTNQRTDDYGGSIENRARFLLEVVDAVAEEIGAGRTGIRLSPVTPANDIFEADPQPLYNYVVEQLGKRNLAFIHVVEGATGGPRDFKQGDKPFDYASFKAAYRNAGGKGLWIANNGYDRQSAIEAVESGKVDAVAFGKAFIANPDLVRRLKNDAPLNAPNQPTFYGGGAEGYTDYPALAQ 371
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371
   Legend:   → Mismatch (orange background)
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    → 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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        O31246_RHIRD | O31246: 5n6g
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(-) Related Entries Specified in the PDB File

4jip 4jiq