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(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS L-PROLINE DEHYDROGENASE
 
Authors :  J. J. Tanner, T. A. White
Date :  17 Feb 06  (Deposition) - 27 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta8-Alpha8-Barrel, Flavoenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. White, N. Krishnan, D. F. Becker, J. J. Tanner
Structure And Kinetics Of Monofunctional Proline Dehydrogenase From Thermus Thermophilus.
J. Biol. Chem. V. 282 14316 2007
PubMed-ID: 17344208  |  Reference-DOI: 10.1074/JBC.M700912200

(-) Compounds

Molecule 1 - PROLINE DEHYDROGENASE/DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
    Chains: A, B
    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: 562
    Expression System Vector Type: PLASMID
    Gene: PROLINE DEHYDROGENASE/DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:133 , MET A:134 , VAL A:161 , GLN A:163 , ARG A:184 , VAL A:186 , LYS A:187 , GLY A:188 , ALA A:189 , TYR A:190 , LYS A:201 , ALA A:225 , THR A:226 , HIS A:227 , ASP A:228 , PRO A:229 , GLN A:252 , LEU A:254 , VAL A:257 , ARG A:258 , TYR A:275 , ARG A:293 , HOH A:2003BINDING SITE FOR RESIDUE FAD A 2001
2AC2SOFTWAREASP B:133 , MET B:134 , VAL B:161 , GLN B:163 , ARG B:184 , VAL B:186 , LYS B:187 , GLY B:188 , ALA B:189 , TYR B:190 , ALA B:225 , THR B:226 , HIS B:227 , ASP B:228 , PRO B:229 , LEU B:254 , VAL B:257 , TYR B:275 , HOH B:2003BINDING SITE FOR RESIDUE FAD B 2002
3AC3SOFTWAREPHE B:129 , ASN B:182 , TYR B:221 , GLU B:250 , ARG B:273BINDING SITE FOR RESIDUE MPD B 371
4AC4SOFTWAREGLY A:30 , ARG A:33 , ARG A:34 , HOH A:2080 , ARG B:151 , PRO B:178BINDING SITE FOR RESIDUE MPD B 372
5AC5SOFTWARELYS A:94 , PHE A:129 , ARG A:131 , ASN A:182 , TYR A:221 , GLU A:250 , ARG A:273BINDING SITE FOR RESIDUE MPD A 373
6AC6SOFTWAREARG A:151 , PRO A:178 , HOH A:2043 , LYS B:194BINDING SITE FOR RESIDUE MPD A 374

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G37)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G37)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G37)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G37)

(-) Exons   (0, 0)

(no "Exon" information available for 2G37)

(-) 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:292
 aligned with PRODH_THET2 | Q72IB8 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:292
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  
          PRODH_THET2     5 LAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAERPEN 296
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhh...eeeeeeee..hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g37 A   5 LAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAERPEN 296
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294  


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with PRODH_THET2 | Q72IB8 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:300
                                  1                                                                                                                                                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
          PRODH_THET2     - ------MNLDLAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAERP 294
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhh...eeeeeee..hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2g37 B  -5 LYFQGHMNLDLAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAERP 294
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
   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 2G37)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G37)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G37)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRODH_THET2 | Q72IB8)
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.
    GO:0004657    proline dehydrogenase activity    Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor.
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.
    GO:0010133    proline catabolic process to glutamate    The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.

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  2g37
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRODH_THET2 | Q72IB8: 2ekg 5m42

(-) Related Entries Specified in the PDB File

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