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(-) Description

Title :  STRUCTURE OF OXIDIZED DEINOCOCCUS RADIODURANS PROLINE DEHYDROGENASE COMPLEXED WITH L-TETRAHYDROFUROIC ACID
 
Authors :  L. Min, J. J. Tanner
Date :  19 Sep 12  (Deposition) - 28 Nov 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.36
Chains :  Asym. Unit :  A,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Keywords :  Beta8-Alpha8-Barrel, Flavoenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Luo, B. W. Arentson, D. Srivastava, D. F. Becker, J. J. Tanner
Crystal Structures And Kinetics Of Monofunctional Proline Dehydrogenase Provide Insight Into Substrate Recognition An Conformational Changes Associated With Flavin Reduction And Product Release.
Biochemistry V. 51 10099 2012
PubMed-ID: 23151026  |  Reference-DOI: 10.1021/BI301312F

(-) Compounds

Molecule 1 - PROLINE DEHYDROGENASE
    Chains: A, C
    EC Number: 1.5.99.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKA8H
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DR_0814, PROLINE DEHYDROGENASE
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AC
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  C

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
3TFB2Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
3TFB1Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL-1Ligand/IonGLYCEROL
3TFB1Ligand/IonTETRAHYDROFURAN-2-CARBOXYLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:135 , MET A:136 , VAL A:164 , GLN A:166 , ARG A:187 , VAL A:189 , LYS A:190 , GLY A:191 , ALA A:192 , TYR A:193 , ALA A:228 , THR A:229 , HIS A:230 , ASP A:231 , GLN A:255 , MET A:256 , LEU A:257 , ILE A:260 , TYR A:278 , ARG A:292 , GLU A:295 , PRO A:297 , TFB A:2002 , HOH A:2104 , HOH A:2115 , HOH A:2128 , HOH A:2136 , HOH A:2183 , HOH A:2210 , HOH A:2350 , HOH A:2377 , HOH A:2380BINDING SITE FOR RESIDUE FAD A 2001
2AC2SOFTWARELYS A:98 , ASP A:135 , TYR A:278 , TYR A:288 , ARG A:291 , ARG A:292 , FAD A:2001 , HOH A:2147BINDING SITE FOR RESIDUE TFB A 2002
3AC3SOFTWARETYR A:94 , TYR A:224 , GLU A:253 , ARG A:276 , HOH A:2295 , HOH A:2310 , HOH A:2362BINDING SITE FOR RESIDUE GOL A 2003
4AC4SOFTWAREASP C:135 , MET C:136 , VAL C:164 , GLN C:166 , ARG C:187 , VAL C:189 , LYS C:190 , GLY C:191 , ALA C:192 , TYR C:193 , ALA C:228 , THR C:229 , HIS C:230 , ASP C:231 , GLN C:255 , MET C:256 , LEU C:257 , ILE C:260 , ARG C:292 , GLU C:295 , PRO C:297 , TFB C:2002 , HOH C:2106 , HOH C:2110 , HOH C:2116 , HOH C:2139 , HOH C:2190 , HOH C:2192 , HOH C:2228 , HOH C:2263BINDING SITE FOR RESIDUE FAD C 2001
5AC5SOFTWARELYS C:98 , ASP C:135 , TYR C:278 , TYR C:288 , ARG C:291 , ARG C:292 , FAD C:2001 , HOH C:2160BINDING SITE FOR RESIDUE TFB C 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H6Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H6Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H6Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H6Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4H6Q)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhh....eeeehhhhh....ee..eehhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh...eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h6q A  17 PQVEQLARQKMWNLAERFVAGESIESAIQAVQALERDGIAGNLDLLGEFIDSPAKCTEFADDVIKLIEAAHAAGIKPYVSIKLSSVGQGKDENGEDLGLTNARRIIAKAKEYGGFICLDMEDHTRVDVTLEQFRTLVGEFGAEHVGTVLQSYLYRSLGDRASLDDLRPNIRMVKGAYLEPATVAYPDKADVDQNYRRLVFQHLKAGNYTNVATHDERIIDDVKRFVLAHGIGKDAFEFQMLYGIRRDLQKQLAAEGYRVRVYLPYGRDWYAYFSRRIAETP 297
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 


Chain C from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhh....eeeehhhhh....ee..eehhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhh..eeeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h6q C  17 PQVEQLARQKMWNLAERFVAGESIESAIQAVQALERDGIAGNLDLLGEFIDSPAKCTEFADDVIKLIEAAHAAGIKPYVSIKLSSVGQGKDENGEDLGLTNARRIIAKAKEYGGFICLDMEDHTRVDVTLEQFRTLVGEFGAEHVGTVLQSYLYRSLGDRASLDDLRPNIRMVKGAYLEPATVAYPDKADVDQNYRRLVFQHLKAGNYTNVATHDERIIDDVKRFVLAHGIGKDAFEFQMLYGIRRDLQKQLAAEGYRVRVYLPYGRDWYAYFSRRIAETP 297
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296
   Legend:   → Mismatch (orange background)
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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 4H6Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H6Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H6Q)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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4h6r