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(-) Description

Title :  STRUCTURE OF REDUCED DEINOCOCCUS RADIODURANS PROLINE DEHYDROGENASE
 
Authors :  L. Min, J. J. Tanner
Date :  19 Sep 12  (Deposition) - 28 Nov 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FDA2Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2FDA1Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FDA1Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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 , THR A:229 , HIS A:230 , LEU A:257 , ILE A:260 , TYR A:278 , ARG A:292 , GLU A:295 , PRO A:297 , HOH A:2101 , HOH A:2131 , HOH A:2158 , HOH A:2182 , HOH A:2242 , HOH A:2297BINDING SITE FOR RESIDUE FDA A 2001
2AC2SOFTWAREARG C:33 , ASP 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 , GLN C:255 , MET C:256 , LEU C:257 , ILE C:260 , TYR C:278 , ARG C:292 , GLU C:295 , PRO C:297 , ACT C:2002 , HOH C:2115 , HOH C:2120BINDING SITE FOR RESIDUE FDA C 2001
3AC3SOFTWARELYS C:98 , TYR C:288 , ARG C:291 , ARG C:292 , FDA C:2001BINDING SITE FOR RESIDUE ACT C 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H6R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H6R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4H6R)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh......hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhh...ee..eehhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhh...eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h6r A  26 KMWNLAERFVAGESIESAIQAVQALERDGIAGNLDLLGEFIDSPAKCTEFADDVIKLIEAAHAAGIKPYVSIKLSSVGQGKDENGEDLGLTNARRIIAKAKEYGGFICLDMEDHTRVDVTLEQFRTLVGEFGAEHVGTVLQSYLYRSLGDRASLDDLRPNIRMVKGAYLEPATVAYPDKADVDQNYRRLVFQHLKAGNYTNVATHDERIIDDVKRFVLAHGIGKDAFEFQMLYGIRRDLQKQLAAEGYRVRVYLPYGRDWYAYFSRRIAETP 297
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295  


Chain C from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhh....ee..eehhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhh.hhh.eeeeee...hhhhhhhhhhh...eeeeeee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h6r C  20 EQLARQKMWNLAERFVAGESIESAIQAVQALERDGIAGNLDLLGEFIDSPAKCTEFADDVIKLIEAAHAAGIKPYVSIKLSSVGQGKDENGEDLGLTNARRIIAKAKEYGGFICLDMEDHTRVDVTLEQFRTLVGEFGAEHVGTVLQSYLYRSLGDRASLDDLRPNIRMVKGAYLEPATVAYPDKADVDQNYRRLVFQHLKAGNYTNVATHDERIIDDVKRFVLAHGIGKDAFEFQMLYGIRRDLQKQLAAEGYRVRVYLPYGRDWYAYFSRRIAETP 297
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289
   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 4H6R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H6R)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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        PRODH_DEIRA | Q9RW55: 4h6q

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4h6q