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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED PROLINE UTILIZATION A (PUTA) FROM GEOBACTER SULFURREDUCENS PCA COMPLEXED WITH ZWITTERGENT 3-12
 
Authors :  H. Singh, J. J. Tanner
Date :  14 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavoenzyme, Rossmann Fold, Aldehyde Dehydrogenase, Flavin Adenine Dinucleotide, Nicotinamide Adenine Dinucleotide, Proline Catabolism, Substrate Channeling, Bifunctional Enzyme, 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  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
12OP1Ligand/Ion(2S)-2-HYDROXYPROPANOIC ACID
2C151Ligand/IonN-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE
3FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4K2Ligand/IonPOTASSIUM ION
5PG43Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP 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 , ALA A:356 , SER A:357 , HIS A:358 , ASN A:359 , LEU A:385 , TYR A:406 , HOH A:2579BINDING SITE FOR RESIDUE FAD A 2001
2AC2SOFTWAREHIS A:639 , HOH A:2536 , ARG B:933 , HOH B:2562BINDING SITE FOR RESIDUE PG4 A 2002
3AC3SOFTWARETHR A:527 , VAL A:528 , GLU A:595 , ILE A:682 , HOH A:2119 , HOH A:2441BINDING SITE FOR RESIDUE K A 2003
4AC4SOFTWAREASP 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 , TYR B:309 , TRP B:310 , TRP B:327 , THR B:328 , ILE B:329 , LYS B:330 , SER B:333 , ALA B:356 , SER B:357 , HIS B:358 , ASN B:359 , GLN B:383 , LEU B:385 , ARG B:422 , GLU B:425 , SER B:431 , PHE B:432 , 2OP B:2006 , HOH B:2170 , HOH B:2282 , HOH B:2461BINDING SITE FOR RESIDUE FAD B 2001
5AC5SOFTWAREHOH A:2236 , HOH A:2344 , LYS B:754 , VAL B:965 , HOH B:2220 , HOH B:2306BINDING SITE FOR RESIDUE PG4 B 2002
6AC6SOFTWAREARG A:933 , HIS B:639 , PHE B:641BINDING SITE FOR RESIDUE PG4 B 2003
7AC7SOFTWARETHR B:527 , VAL B:528 , GLU B:595 , ILE B:682 , HOH B:2137 , HOH B:2359BINDING SITE FOR RESIDUE K B 2004
8AC8SOFTWAREPHE B:76BINDING SITE FOR RESIDUE C15 B 2005
9AC9SOFTWARELYS B:203 , ALA B:308 , TYR B:418 , ARG B:421 , ARG B:422 , FAD B:2001 , HOH B:2182BINDING SITE FOR RESIDUE 2OP B 2006

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NMC)

(-) 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:941
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhh...hhh.eeeeee...hhhhhhhhhhhhh.eeeeeee.hhhhhhhhh.....hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh......eee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhheeeee.............eeee.....hhhhh......eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nmc A    4 SELNTKIVNRGKEFFGSQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMSTGAKVAGMLGSFGGAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLERLLEDPAVTVERERAARKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDW 1002
                                    13      ||49        59        69        79        89        99       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|      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 
                                           20|                                                                                                                                                                                                                                                                                                                                                                                 419|              461|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                            47                                                                                                                                                                                                                                                                                                                                                                                  444               470                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:969
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh..hhhhhhhh...hhhhhh.hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee......eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh.....eee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhh.........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
                4nmc B    3 NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGGGAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDD 1001
                                    12        22        32        42        52        62        72    || 104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992         
                                                                                                     77|                                                                                                                                                                                                                                                                                                                                                                       462|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                     100                                                                                                                                                                                                                                                                                                                                                                        471
   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 4NMC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4nm9 4nma 4nmb 4nmd 4nme 4nmf