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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLINE UTILIZATION A (PUTA) FROM GEOBACTER SULFURREDUCENS PCA INACTIVATED BY N-PROPARGYLGLYCINE
 
Authors :  H. Singh, J. J. Tanner
Date :  14 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
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
    Chains: A, B
    EC Number: 1.5.99.8, 1.5.1.12, 1.2.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21-AI
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PUTA, GSU3395
    Organism Scientific: GEOBACTER SULFURREDUCENS
    Organism Taxid: 243231
    Strain: ATCC 51573 / DSM 12127 / PCA
    Synonym: PROLINE UTILIZATION A, PUTA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2P5F2Ligand/IonN-PROPARGYLGLYCINE-MODIFIED FLAVIN ADENINE DINUCLEOTIDE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
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 , 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 , PHE A:432 , HOH A:1352 , HOH A:1375 , HOH A:1525BINDING SITE FOR RESIDUE P5F A 1101
02AC2SOFTWARETYR A:248 , TRP A:322 , ASP A:485 , HOH A:1205 , HOH A:1495 , HOH A:1649BINDING SITE FOR RESIDUE EDO A 1102
03AC3SOFTWAREGLU A:609 , PHE A:613 , LEU A:951 , VAL A:952 , GLN A:955 , PRO A:956 , PHE A:957 , ALA A:969 , HOH A:1400BINDING SITE FOR RESIDUE EDO A 1103
04AC4SOFTWAREALA A:910 , ASN A:911 , THR A:913 , PHE A:915 , ALA A:916 , ARG A:937 , VAL A:938 , ARG A:961 , HOH A:1233 , HOH A:1313BINDING SITE FOR RESIDUE EDO A 1104
05AC5SOFTWARETRP A:327 , GLU A:332 , ALA A:336 , ARG A:339 , ARG A:458 , HOH A:1327BINDING SITE FOR RESIDUE EDO A 1105
06AC6SOFTWAREGLU A:636 , ASN A:987 , ARG B:945BINDING SITE FOR RESIDUE EDO A 1106
07AC7SOFTWAREPHE A:513 , LEU A:699 , PRO A:700 , GLU A:701 , GLY A:702 , VAL A:703 , PHE A:704BINDING SITE FOR RESIDUE EDO A 1107
08AC8SOFTWARETYR A:616 , ARG A:619 , GLU A:620 , GLU A:953 , HOH A:1592BINDING SITE FOR RESIDUE EDO A 1108
09AC9SOFTWAREPRO A:477 , PHE A:478 , ASN A:479 , GLU A:615 , ARG A:619BINDING SITE FOR RESIDUE EDO A 1109
10BC1SOFTWARELYS 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 , HOH B:1599 , HOH B:1601 , HOH B:1602BINDING SITE FOR RESIDUE P5F B 1101
11BC2SOFTWAREASP B:770 , ASP B:803 , ALA B:804 , LYS B:901 , HOH B:1305BINDING SITE FOR RESIDUE EDO B 1102
12BC3SOFTWAREASP A:770 , ASP A:803 , ALA A:804 , LYS A:901 , HOH A:1202BINDING SITE FOR RESIDUE EDO B 1103
13BC4SOFTWAREGLU B:609 , PHE B:613 , ALA B:950 , LEU B:951 , VAL B:952 , GLN B:955 , PHE B:957 , ALA B:969 , GLY B:970 , HOH B:1276BINDING SITE FOR RESIDUE EDO B 1104
14BC5SOFTWARETYR B:248 , TRP B:322 , ASP B:485 , HOH B:1215 , HOH B:1331BINDING SITE FOR RESIDUE EDO B 1105
15BC6SOFTWAREGLN A:319 , ARG A:945 , GLU B:636BINDING SITE FOR RESIDUE EDO B 1106
16BC7SOFTWAREASN B:911 , PHE B:915 , ARG B:937 , VAL B:938 , ARG B:961 , HOH B:1251BINDING SITE FOR RESIDUE EDO B 1107
17BC8SOFTWARELYS A:755 , LYS B:755 , ILE B:756 , VAL B:965 , HOH B:1286BINDING SITE FOR RESIDUE EDO B 1108
18BC9SOFTWAREPHE B:513 , LEU B:699 , PRO B:700 , GLU B:701 , GLY B:702 , VAL B:703 , PHE B:704 , HOH B:1207 , HOH B:1663BINDING SITE FOR RESIDUE EDO B 1109

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NME)

(-) 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:972
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhh...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......eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4nme A    0 SMLNSELNTKIVNRGKEFFGSIPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                     9        19 ||     33        43        53        63        73        83 ||    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       393       403       413       423       433       443       453       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001  
                                                21|                                                         85|                                                                                                                                                                                                                                                                                          388|                                                                  461|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                 26                                                         103                                                                                                                                                                                                                                                                                           392                                                                   470                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:978
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh......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
                4nme B    3 NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                    12        22        32        42        52        62        72        82   ||  107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457   ||  475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995        
                                                                                                              86|                                                                                                                                                                                                                                                                                                                                                                    461|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                              102                                                                                                                                                                                                                                                                                                                                                                     470
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  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 4NME)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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        Q746X3_GEOSL | Q746X3: 4nm9 4nma 4nmb 4nmc 4nmd 4nmf

(-) Related Entries Specified in the PDB File

4nm9 4nma 4nmb 4nmc 4nmd 4nmf