Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A DYE-LINKED L-PROLINE DEHYDROGENASE MUTANT FROM THE AEROBIC HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX
 
Authors :  H. Sakuraba, T. Ohshima, T. Satomura, K. Yoneda
Date :  29 Mar 12  (Deposition) - 25 Apr 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dinucleotide-Binding Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sakuraba, T. Satomura, R. Kawakami, K. Kim, Y. Hara, K. Yoneda, T. Ohshima
Crystal Structure Of Novel Dye-Linked L-Proline Dehydrogenase From Hyperthermophilic Archaeon Aeropyrum Pernix
J. Biol. Chem. V. 287 20070 2012
PubMed-ID: 22511758  |  Reference-DOI: 10.1074/JBC.M111.319038

(-) Compounds

Molecule 1 - PUTATIVE OXIDOREDUCTASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-427
    Mutation: YES
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 272557
    Strain: K1
    Synonym: L-PROLINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , GLY A:12 , VAL A:13 , VAL A:14 , ASP A:34 , ALA A:35 , GLY A:42 , ASP A:43 , SER A:44 , ARG A:46 , SER A:47 , MET A:48 , ALA A:50 , ARG A:182 , ARG A:183 , VAL A:184 , ALA A:229 , ALA A:230 , GLY A:231 , TRP A:233 , ARG A:252 , GLN A:302 , GLY A:350 , HIS A:351 , TYR A:352 , THR A:376 , GLY A:378 , SER A:379 , GLY A:380 , ILE A:381 , MET A:382 , ACT A:1002 , HOH A:1107 , HOH A:1109 , HOH A:1110 , HOH A:1116 , HOH A:1144 , HOH A:1153 , HOH A:1175 , HOH A:1185BINDING SITE FOR RESIDUE FAD A 1001
2AC2SOFTWAREASP A:43 , GLY A:231 , VAL A:232 , HIS A:351 , ASP A:353 , THR A:376 , FAD A:1001 , HOH A:1185BINDING SITE FOR RESIDUE ACT A 1002
3AC3SOFTWAREGLY A:231 , VAL A:232 , ASN A:235 , THR A:245 , SER A:247 , ARG A:248 , PRO A:249 , ASP A:353BINDING SITE FOR RESIDUE EDO A 1003
4AC4SOFTWAREILE A:243 , ASP A:244 , PHE A:246 , TRP A:366 , LEU A:416 , PHE B:311BINDING SITE FOR RESIDUE EDO A 1004
5AC5SOFTWAREGLY B:10 , GLY B:12 , VAL B:13 , VAL B:14 , ASP B:34 , ALA B:35 , GLY B:42 , ASP B:43 , SER B:44 , ARG B:46 , SER B:47 , MET B:48 , ALA B:49 , ALA B:50 , ARG B:183 , VAL B:184 , ALA B:229 , ALA B:230 , GLY B:231 , TRP B:233 , ARG B:252 , GLN B:302 , GLY B:350 , HIS B:351 , TYR B:352 , THR B:376 , GLY B:378 , SER B:379 , GLY B:380 , ILE B:381 , MET B:382 , ACT B:1002 , HOH B:1104 , HOH B:1110 , HOH B:1115 , HOH B:1118 , HOH B:1120 , HOH B:1166 , HOH B:1185BINDING SITE FOR RESIDUE FAD B 1001
6AC6SOFTWAREASP B:43 , GLY B:231 , VAL B:232 , HIS B:351 , ASP B:353 , THR B:376 , FAD B:1001BINDING SITE FOR RESIDUE ACT B 1002
7AC7SOFTWAREGLY B:231 , VAL B:232 , ASN B:235 , THR B:245 , SER B:247 , ARG B:248 , PRO B:249 , ASP B:353BINDING SITE FOR RESIDUE EDO B 1003
8AC8SOFTWAREILE B:243 , ASP B:244 , PHE B:363BINDING SITE FOR RESIDUE EDO B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VQR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:200 -Pro A:201
2Glu B:200 -Pro B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VQR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VQR)

(-) Exons   (0, 0)

(no "Exon" information available for 3VQR)

(-) Sequences/Alignments

Asymmetric/Biological 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:425
 aligned with Q9YCJ0_AERPE | Q9YCJ0 from UniProtKB/TrEMBL  Length:428

    Alignment length:425
                                    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       381       391       401       411       421     
         Q9YCJ0_AERPE     2 PRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSMAAFRTFFSSTMNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGMNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRMVFRVSASTEGLRRIMREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVALGMESVELYGGVEMPVKWMGLEGRRYEQERL 426
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhh..eeee........hhhhh...eee....hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhh........eeeehhhhhhhhhh.......hhhhhhhh.....eeeee..eee.hhhhhhhhhhhhhhhhh.eee....eeeeeeee...............eeeeeeee....eeeeeeeeee.hhhhhhhhhhhhh....eeeeeeeeeeee..hhhhhhhhhhh.........eeee...eeeeeehhh.eeeee.................hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....eee......eeeee....hhhhhhhhhhhhhhhhhh...eee.....eee.hhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqr A   2 PRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSMAAFRTFFSSTMNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGMNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRMVFRVSASTEGLRRIMREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVALGMESVELYGGVEMPVKWMGLEGRRYEQERL 426
                                    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       381       391       401       411       421     


Chain B from PDB  Type:PROTEIN  Length:425
 aligned with Q9YCJ0_AERPE | Q9YCJ0 from UniProtKB/TrEMBL  Length:428

    Alignment length:425
                                    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       381       391       401       411       421     
         Q9YCJ0_AERPE     2 PRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSMAAFRTFFSSTMNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGMNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRMVFRVSASTEGLRRIMREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVALGMESVELYGGVEMPVKWMGLEGRRYEQERL 426
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhh..eeeee.......hhhhh...eee....hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhh.....eeeehhhhhhhhhh........hhhhhhh.....eeeee..eee.hhhhhhhhhhhhhhhhh.eeee...eeeeeeee...............eeeeeeee....eeeeeeeeee.hhhhhhhhhhhhh....eeeeeeeeeeee..hhhhhhhhhhh.........eeee...eeeeeehhh.eeeee.................hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....eeehhhhh.eeeee....hhhhhhhhhhhhhhhhhh...eee.....eee.hhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqr B   2 PRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSMAAFRTFFSSTMNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGMNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRMVFRVSASTEGLRRIMREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVALGMESVELYGGVEMPVKWMGLEGRRYEQERL 426
                                    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       381       391       401       411       421
   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 3VQR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VQR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VQR)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9YCJ0_AERPE | Q9YCJ0)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:200 - Pro A:201   [ RasMol ]  
    Glu B:200 - Pro B:201   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3vqr
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9YCJ0_AERPE | Q9YCJ0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9YCJ0_AERPE | Q9YCJ0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9YCJ0_AERPE | Q9YCJ0: 3axb

(-) Related Entries Specified in the PDB File

3axb STRUCTURE OF A DYE-LINKED L-PROLINE DEHYDROGENASEFROM THE AEROBIC HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX