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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLINE UTILIZATION A (PUTA) FROM GEOBACTER SULFURREDUCENS PCA REDUCED WITH DITHIONITE
 
Authors :  H. Singh, J. J. Tanner
Date :  14 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
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  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1EDO14Ligand/Ion1,2-ETHANEDIOL
2FDA2Ligand/IonDIHYDROFLAVINE-ADENINE DINUCLEOTIDE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP 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 , VAL A:384 , LEU A:385 , TYR A:406 , PHE A:432 , HOH A:1355 , HOH A:1495BINDING SITE FOR RESIDUE FDA A 1101
02AC2SOFTWARETYR A:248 , TRP A:322 , ASP A:485 , THR A:487 , HOH A:1204 , HOH A:1471 , HOH A:1613BINDING SITE FOR RESIDUE EDO A 1102
03AC3SOFTWARETRP A:327 , GLU A:332 , ALA A:336 , ARG A:339 , ARG A:458 , HOH A:1329BINDING SITE FOR RESIDUE EDO A 1103
04AC4SOFTWARETYR A:616 , ARG A:619 , GLU A:620 , GLU A:953 , HOH A:1644BINDING SITE FOR RESIDUE EDO A 1104
05AC5SOFTWAREGLU A:636 , ASN A:987 , GLN B:319 , ARG B:945BINDING SITE FOR RESIDUE EDO A 1105
06AC6SOFTWAREASP A:770 , ASP A:803 , ALA A:804 , LYS A:901 , HOH A:1201BINDING SITE FOR RESIDUE EDO A 1106
07AC7SOFTWAREGLN A:319 , ARG A:945 , GLU B:636BINDING SITE FOR RESIDUE EDO A 1107
08AC8SOFTWAREGLU A:609 , PHE A:613 , ALA A:950 , LEU A:951 , VAL A:952 , GLN A:955 , PRO A:956 , PHE A:957 , ALA A:969 , HOH A:1397BINDING SITE FOR RESIDUE EDO A 1108
09AC9SOFTWAREASP B:244 , MET B:245 , VAL B:274 , GLN B:276 , TYR B:278 , ARG B:303 , 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 , SER B:357 , HIS B:358 , ASN B:359 , GLN B:383 , VAL B:384 , LEU B:385 , TYR B:406 , GLU B:425 , SER B:431 , PHE B:432 , HOH B:1547 , HOH B:1548BINDING SITE FOR RESIDUE FDA B 1101
10BC1SOFTWAREGLU B:609 , PHE B:613 , ALA B:950 , LEU B:951 , VAL B:952 , GLN B:955 , PRO B:956 , PHE B:957 , ALA B:969 , HOH B:1272BINDING SITE FOR RESIDUE EDO B 1102
11BC2SOFTWARETYR B:248 , TRP B:322 , ASP B:485 , HOH B:1215 , HOH B:1316 , HOH B:1328BINDING SITE FOR RESIDUE EDO B 1103
12BC3SOFTWARETYR B:616 , ARG B:619 , GLU B:620 , GLU B:953 , HOH B:1658BINDING SITE FOR RESIDUE EDO B 1104
13BC4SOFTWAREGLU A:346 , ASN A:347 , ASP B:550 , HOH B:1660BINDING SITE FOR RESIDUE EDO B 1105
14BC5SOFTWAREPHE B:513 , GLY B:516 , LEU B:699 , PRO B:700 , GLU B:701 , GLY B:702 , VAL B:703 , PHE B:704 , HOH B:1207 , HOH B:1605BINDING SITE FOR RESIDUE EDO B 1106
15BC6SOFTWARELYS A:755 , LYS B:755 , ILE B:756 , VAL B:965 , HIS B:977 , HOH B:1283BINDING SITE FOR RESIDUE EDO B 1107
16BC7SOFTWAREALA B:910 , ASN B:911 , THR B:913 , PHE B:915 , ALA B:916 , ARG B:937 , VAL B:938 , HOH B:1247BINDING SITE FOR RESIDUE EDO B 1108

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NMD)

(-) 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:979
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhh.hhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh......eee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhheeeee.............eeee.....hhhhh......eeeeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhh...eeee................hhhhh.........hhhh.eeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4nmd A    0 SMLNSELNTKIVNRGKEFFGSIPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAAKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                     9        19 ||     33        43        53        63        73        83  ||   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458    || 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         
                                                21|                                                          86|                                                                                                                                                                                                                                                                                                                                                                      463|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                 26                                                          102                                                                                                                                                                                                                                                                                                                                                                       470                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:980
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhh.hhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.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
                4nmd B    3 NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARAAKGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 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     ||473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003
                                                                                                              86|                                                                                                                                                                                                                                                                                                                                                                      463|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                              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 4NMD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4nmc 4nme 4nmf

(-) Related Entries Specified in the PDB File

4nm9 4nma 4nmb 4nmc 4nme 4nmf