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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLINE UTILIZATION A (PUTA) FROM GEOBACTER SULFURREDUCENS PCA INACTIVATED BY N-PROPARGYLGLYCINE AND COMPLEXED WITH MENADIONE BISULFITE
 
Authors :  H. Singh, J. J. Tanner
Date :  14 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavoenzyme, Rossmann Fold, Aldehyde Dehydrogenase, Flavin Adenine Dinucleotide, Nicotinamide Adenine Dinucleotide, Proline Catabolism, Substrate Channeling, Bifunctional Enzyme, Mechanism-Based Inactivation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Singh, B. W. Arentson, D. F. Becker, J. J. Tanner
Structures Of The Puta Peripheral Membrane Flavoenzyme Reveal A Dynamic Substrate-Channeling Tunnel And The Quinone-Binding Site.
Proc. Natl. Acad. Sci. Usa V. 111 3389 2014
PubMed-ID: 24550478  |  Reference-DOI: 10.1073/PNAS.1321621111

(-) Compounds

Molecule 1 - PROLINE DEHYDROGENASE AND DELTA-1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
    ChainsA, B
    EC Number1.5.99.8, 1.5.1.12, 1.2.1.88
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21-AI
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GenePUTA, GSU3395
    Organism ScientificGEOBACTER SULFURREDUCENS
    Organism Taxid243231
    StrainATCC 51573 / DSM 12127 / PCA
    SynonymPROLINE UTILIZATION A, PUTA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
12L32Ligand/Ion(2R)-2-METHYL-1,4-DIOXO-1,2,3,4-TETRAHYDRONAPHTHALENE-2-SULFONIC ACID
22LB1Ligand/Ion(2S)-2-METHYL-1,4-DIOXO-1,2,3,4-TETRAHYDRONAPHTHALENE-2-SULFONIC ACID
3EDO8Ligand/Ion1,2-ETHANEDIOL
4P5F2Ligand/IonN-PROPARGYLGLYCINE-MODIFIED FLAVIN ADENINE DINUCLEOTIDE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:203 , ASP A:244 , MET A:245 , VAL A:274 , GLN A:276 , TYR A:278 , ARG A:303 , VAL A:305 , LYS A:306 , GLY A:307 , ALA A:308 , TYR A:309 , TRP A:310 , TRP A:327 , THR A:328 , ILE A:329 , LYS A:330 , SER A:333 , SER A:357 , HIS A:358 , ASN A:359 , GLN A:383 , LEU A:385 , TYR A:406 , GLU A:425 , GLU A:430 , PHE A:432 , 2L3 A:1102 , HOH A:1500 , HOH A:1658BINDING SITE FOR RESIDUE P5F A 1101
02AC2SOFTWAREASP A:145 , LYS A:203 , ALA A:308 , TYR A:309 , TYR A:406 , TYR A:418 , ARG A:421 , ARG A:422 , P5F A:1101 , HOH A:1633BINDING SITE FOR RESIDUE 2L3 A 1102
03AC3SOFTWARETRP A:327 , GLU A:332 , ALA A:336 , ARG A:339 , ARG A:458 , HOH A:1322BINDING SITE FOR RESIDUE EDO A 1103
04AC4SOFTWARELYS A:316 , GLN A:319 , HOH A:1583 , ASN B:987BINDING SITE FOR RESIDUE EDO A 1104
05AC5SOFTWARETYR A:248 , TRP A:322 , ASP A:485 , HOH A:1204 , HOH A:1473 , HOH A:1609BINDING SITE FOR RESIDUE EDO A 1105
06AC6SOFTWARETYR A:616 , ARG A:619 , GLU A:620 , GLU A:953 , HOH A:1661BINDING SITE FOR RESIDUE EDO A 1106
07AC7SOFTWAREASP A:770 , ASP A:803 , ALA A:804 , LYS A:901BINDING SITE FOR RESIDUE EDO A 1107
08AC8SOFTWARELYS B:203 , ASP B:244 , MET B:245 , VAL B:274 , GLN B:276 , TYR B:278 , ARG B:303 , VAL B:305 , LYS B:306 , GLY B:307 , ALA B:308 , TRP B:310 , TRP B:327 , THR B:328 , ILE B:329 , LYS B:330 , SER B:333 , SER B:357 , HIS B:358 , ASN B:359 , GLN B:383 , LEU B:385 , TYR B:406 , GLU B:425 , GLU B:430 , SER B:431 , PHE B:432 , 2L3 B:1102 , 2LB B:1103 , HOH B:1566 , HOH B:1567BINDING SITE FOR RESIDUE P5F B 1101
09AC9SOFTWAREASP B:145 , LYS B:203 , ALA B:308 , TYR B:309 , TYR B:406 , TYR B:418 , ARG B:421 , ARG B:422 , P5F B:1101BINDING SITE FOR RESIDUE 2L3 B 1102
10BC1SOFTWARELYS B:203 , TYR B:309 , LEU B:385 , TYR B:418 , ARG B:421 , P5F B:1101BINDING SITE FOR RESIDUE 2LB B 1103
11BC2SOFTWARETYR B:616 , ARG B:619 , GLU B:620 , HOH B:1632BINDING SITE FOR RESIDUE EDO B 1104
12BC3SOFTWARETYR B:248 , TRP B:322 , ASP B:485 , HOH B:1215 , HOH B:1315 , HOH B:1327BINDING SITE FOR RESIDUE EDO B 1105
13BC4SOFTWAREARG A:945 , GLU B:636BINDING SITE FOR RESIDUE EDO B 1106

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NMF)

(-) 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:973
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhh.hhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhheeeee.............eeee.....hhhhh......eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nmf A    3 NSELNTKIVNRGKEFFGSPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAQIERLLEDPAVTVERERAARAARKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                    12       |27        37        47        57        67        77       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432    || 445       455       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000   
                                            20|                                                          86|                                                                                                                                                                                                                                                                                                                                            437|                   463|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                             26                                                          102                                                                                                                                                                                                                                                                                                                                             441                    469                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:979
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhh.hhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhh.eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhheeeee.............eeee.....hhhhh......eeeeeee.hhhhhhhhhh...ee.eeeee..hhhhhhhhhhhh...eeee................ee............hhhh.eeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nmf B    5 ELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAARKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                    14        24        34        44        54        64        74        84 ||    109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459   ||  474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994         
                                                                                                            86|                                                                                                                                                                                                                                                                                                                                                                      463|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                                                                                                            102                                                                                                                                                                                                                                                                                                                                                                       469                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      

   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 4NMF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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        Q746X3_GEOSL | Q746X34nm9 4nma 4nmb 4nmc 4nmd 4nme

(-) Related Entries Specified in the PDB File

4nm9 4nma 4nmb 4nmc 4nmd 4nme