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(-) Description

Title :  STRUCTURE OF THERMUS THERMOPHILUS PROLINE DEHYDROGENASE INACTIVATED BY N-PROPARGYLGLYCINE
 
Authors :  T. A. White, J. J. Tanner
Date :  23 Mar 07  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Proline Dehydrogenase, Flavoenzyme, Prodh, Beta-Alpha-Barrel, Suicide Inhibitor, Inactivation, Flavocyanine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. White, W. H. Johnson, C. P. Whitman, J. J. Tanner
Structural Basis For The Inactivation Of Thermus Thermophilus Proline Dehydrogenase By N-Propargylglycine
Biochemistry V. 47 5573 2008
PubMed-ID: 18426222  |  Reference-DOI: 10.1021/BI800055W

(-) 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
    Synonym: L-PROLINE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2LYX2Mod. Amino AcidN''-(2-COENZYME A)-PROPANOYL-LYSINE
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2LYX2Mod. Amino AcidN''-(2-COENZYME A)-PROPANOYL-LYSINE
3MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2LYX1Mod. Amino AcidN''-(2-COENZYME A)-PROPANOYL-LYSINE
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2LYX1Mod. Amino AcidN''-(2-COENZYME A)-PROPANOYL-LYSINE
3MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:133 , MET A:134 , GLN A:163 , ARG A:184 , LYS A:187 , GLY A:188 , ALA A:189 , THR A:226 , HIS A:227 , ASP A:228 , PRO A:229 , GLN A:252 , TYR A:275 , HOH A:2023 , HOH A:2173BINDING SITE FOR RESIDUE FAD A 2001
2AC2SOFTWAREASP B:133 , MET B:134 , GLN B:163 , ARG B:184 , LYS B:187 , GLY B:188 , ALA B:189 , ALA B:225 , THR B:226 , HIS B:227 , ASP B:228 , PRO B:229 , GLN B:252 , TYR B:275 , HOH B:2089BINDING SITE FOR RESIDUE FAD B 2002
3AC3SOFTWAREPHE B:129 , ARG B:131 , ASN B:182 , TYR B:221 , GLU B:250 , ARG B:273BINDING SITE FOR RESIDUE MPD B 1371
4AC4SOFTWAREGLY A:30 , ARG A:33 , ARG A:34 , HOH A:2126 , ARG B:151 , TYR B:179BINDING SITE FOR RESIDUE MPD B 1372
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 1373
6AC6SOFTWAREARG A:151 , HOH A:2151 , LYS B:194BINDING SITE FOR RESIDUE MPD A 1374

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EKG)

(-) 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:289
 aligned with PRODH_THET2 | Q72IB8 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:289
                                    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         
          PRODH_THET2     5 LAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAER 293
               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..eeeeeeeee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekg A   5 LAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLkLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAER 293
                                    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         
                                                                                                                         99-LYX                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:299
 aligned with PRODH_THET2 | Q72IB8 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:299
                                  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         
          PRODH_THET2     - ------MNLDLAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLKLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAER 293
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhh...eeeeeee..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ekg B  -5 LYFQGHMNLDLAYRSFVLGVAGHPQVERLIKHRAKGLVRRYVAGETLEEALKAAEALEREGVHAILDLLGEMVRTEEEARAFQRGLLELVWALAGKPWPKYISLkLTQLGLDLSEDLALALLREVLREAEPRGVFVRLDMEDSPRVEATLRLYRALREEGFSQVGIVLQSYLYRTEKDLLDLLPYRPNLRLVKGAYREPKEVAFPDKRLIDAEYLHLGKLALKEGLYVAFATHDPRIIAELKRYTEAMGIPRSRFEFQFLYGVRPEEQRRLAREGYTVRAYVPYGRDWYPYLTRRIAER 293
                                     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         
                                                                                                                                   99-LYX
   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 2EKG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric 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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 Related Entries

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

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        PRODH_THET2 | Q72IB8: 2g37 5m42

(-) Related Entries Specified in the PDB File

2g37 STRUCTURE OF THERMUS THERMOPHILUS L-PROLINE DEHYDROGENASE