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(-) Description

Title :  STRUCTURE OF A DYE-LINKED L-PROLINE DEHYDROGENASE FROM THE AEROBIC HYPERTHERMOPHILIC ARCHAEON, AEROPYRUM PERNIX
 
Authors :  H. Sakuraba, T. Ohshima, T. Satomura, K. Yoneda, Y. Hara
Date :  01 Apr 11  (Deposition) - 04 Apr 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AEROPYRUM PERNIX
    Organism Taxid: 56636
    Synonym: L-PROLINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE10Mod. Amino AcidSELENOMETHIONINE
4PRO1Mod. Amino AcidPROLINE
Biological Unit 1 (4, 36)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE20Mod. Amino AcidSELENOMETHIONINE
4PRO2Mod. Amino AcidPROLINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:52 , TYR A:88 , LEU A:289 , TYR A:352 , GLY A:378 , SER A:379 , MSE A:382 , LEU A:428 , FAD A:1001 , HOH A:4004BINDING SITE FOR RESIDUE PRO A 2001
2AC2SOFTWAREGLY 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 , MSE A:48 , ALA A:49 , ALA A:50 , ARG A:182 , ARG A:183 , VAL A:184 , ALA A:229 , ALA A:230 , TRP A:233 , VAL A:254 , GLY A:350 , HIS A:351 , TYR A:352 , THR A:376 , GLY A:378 , SER A:379 , GLY A:380 , ILE A:381 , MSE A:382 , PRO A:2001 , HOH A:4002 , HOH A:4005 , HOH A:4010 , HOH A:4024 , HOH A:4025 , HOH A:4029 , HOH A:4065BINDING SITE FOR RESIDUE FAD A 1001
3AC3SOFTWAREPHE A:157 , LEU A:158 , ARG A:291 , TRP A:300 , HOH A:4099 , HOH A:4157BINDING SITE FOR RESIDUE EDO A 3001
4AC4SOFTWAREPRO A:365 , TRP A:366 , EDO A:3005 , HOH A:4080BINDING SITE FOR RESIDUE EDO A 3002
5AC5SOFTWAREPRO A:201 , LEU A:202 , PRO A:203 , ASP A:305 , LEU A:307 , HOH A:4095 , HOH A:4169BINDING SITE FOR RESIDUE EDO A 3003
6AC6SOFTWAREGLY 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 3004
7AC7SOFTWAREILE A:354 , SER A:355 , PHE A:356 , GLN A:423 , EDO A:3002 , EDO A:3006 , HOH A:4057 , HOH A:4166BINDING SITE FOR RESIDUE EDO A 3005
8AC8SOFTWAREILE A:243 , ASP A:244 , TRP A:366 , EDO A:3005BINDING SITE FOR RESIDUE EDO A 3006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:200 -Pro A:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AXB)

(-) 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:429
 aligned with Q9YCJ0_AERPE | Q9YCJ0 from UniProtKB/TrEMBL  Length:428

    Alignment length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     428 
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       | 
        Q9YCJ0_AERPE      1 MPRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSMAAFRTFFSSTMNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGMNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRMVFRVSASTEGLRRIMREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGIMKSDSIGRVAAAVALGMESVELYGGVEMPVKWMGLEGRRYEQERLVL-    -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhhhh..eeeee.......hhhhh...eee....hhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhh........eeeehhhhhhhhhh........hhhhhhh.....eeeee..eee.hhhhhhhhhhhhhhhh..eeee...eeeeeeee...............eeeeeeee....eeeeeeeeee.hhhhhhhhhhhhh....eeeeeeeeeeee..hhhhhhhhhhh.........eeee...eeeeee....eeeeee................hhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.....eeehhhhh.eeeee.....hhhhhhhhhhhhhhhhh...eee.....eee.hhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3axb A    1 mPRFDYVVVGAGVVGLAAAYYLKVWSGGSVLVVDAGHAPGSGDSGRSmAAFRTFFSSTmNRLVAGSTVRLFEDAQRGGEDLGLVKSGYLFVYDRERWREVEEPLREAGEEGRDYLIIPPEELERRLGmNTRVSDGEEAEVLGVGDVEGAVLIRSAGFLDAEKVVDYYYRRASGAGVEFIFGRRVVGVELKPRVELGIEGEPLPWQEARASAAVLSDGTRVEVGEKLVVAAGVWSNRLLNPLGIDTFSRPKKRmVFRVSASTEGLRRImREGDLAGAGAPPLIILPKRVLVRPAPREGSFWVQLSDNLGRPFALEEDPQPEEHYYSLAILPILSLYLPQFQDAYPSGGWAGHYDISFDANPVVFEPWESGIVVAAGTSGSGImKSDSIGRVAAAVALGmESVELYGGVEmPVKWmGLEGRRYEQERLVLP 2001
                            |       10        20        30        40       |50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250  |    260       270       280       290       300       310       320       330       340       350       360       370       380 |     390       400       410   |   420       ||
                            |                                             48-MSE     59-MSE                                                              128-MSE                                                                                                                      253-MSE        268-MSE                                                                                                           382-MSE         398-MSE    409-MSE|           428|
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                                      414-MSE       2001
   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 3AXB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (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.

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 Related Entries

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        Q9YCJ0_AERPE | Q9YCJ0: 3vqr

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