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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLINE UTILIZATION A (PUTA) FROM GEOBACTER SULFURREDUCENS PCA IN COMPLEX WITH L-LACTATE
 
Authors :  H. Singh, S. C. Almo, J. J. Tanner
Date :  14 Nov 13  (Deposition) - 19 Feb 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
12OP2Ligand/Ion(2S)-2-HYDROXYPROPANOIC ACID
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
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 , ARG A:422 , GLU A:425 , SER A:431 , PHE A:432 , 2OP A:2002 , HOH A:2182 , HOH A:2188 , HOH A:2207 , HOH A:2379BINDING SITE FOR RESIDUE FAD A 2001
2AC2SOFTWARELYS A:203 , TYR A:418 , ARG A:421 , ARG A:422 , FAD A:2001 , HOH A:2207BINDING SITE FOR RESIDUE 2OP A 2002
3AC3SOFTWAREGLU A:609 , PHE A:613 , PHE A:656 , SER A:794 , GLY A:949 , ALA A:950 , PHE A:957 , HOH A:2240 , HOH A:2253BINDING SITE FOR RESIDUE MES A 2003
4AC4SOFTWAREASP B:244 , MET B:245 , 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 , TYR B:406 , ARG B:422 , GLU B:425 , SER B:431 , PHE B:432 , 2OP B:2002 , HOH B:2146 , HOH B:2201BINDING SITE FOR RESIDUE FAD B 2001
5AC5SOFTWARELYS B:203 , ALA B:308 , TYR B:418 , ARG B:421 , ARG B:422 , FAD B:2001 , HOH B:2188BINDING SITE FOR RESIDUE 2OP B 2002
6AC6SOFTWAREGLU B:609 , PHE B:613 , PHE B:656 , ILE B:660 , SER B:794 , THR B:948 , GLY B:949 , ALA B:950 , HOH B:2108 , HOH B:2253BINDING SITE FOR RESIDUE MES B 2003

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NMB)

(-) 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:976
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh....eeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........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
                4nmb A    3 NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERAARLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 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   ||  477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      
                                                                                                              86|                                                                                                                                                                                                                                                                                                                                                                    461|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                              102                                                                                                                                                                                                                                                                                                                                                                     472                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:976
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh....eeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh..hhh.eeeeee...hhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhh...hhhhhh.hhhhhhhhhh.................hhhhhhhhhhhhhhhhh...eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh......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
                4nmb B    3 NSELNTKIVNRGKEFFGSISGEKPSLFNKGAWMGKAMDWSMQNEQFKIQMFRFVDVFPSLTTSKLLTEHIREYFGNEQDMPAFMSTAVLNKVLTSNIEEMARQFIVGETTKEAVKNLEKLRKDGFAAVVDVLGEATLSEEEAEVYTNTYLELLEALKKEQGSWKGLPGKGGDPGLDWGHAPKVNIAVKPTALFCLANPQDFEGSVVAILDRMRRIFKKVMELNGFLCIDMESYRHKEIILEVFRRLKLEYRDYPHLGIVLQAYLKDNDKDLDDLLAWAKEHKVQISVRLVKGAYWDYETVKAKQNDWEVPVWTIKAESDAAYERQARKILENHQICHFACASHNIRTISAVMEMARELNVPEDRYEFQVLYGMAEPVRKGILKVAGRIRLYAPYGNMVPGMGYLVRRLLENTANESFLRQSFAEDAQIERLLEDPAVTVERERGLGGLPPFNNEAMVDFTRADHRAAFPKHIAQVRTQLGKTYPLFINGKEVRTNDLIPTVNPNKPSEVLGQICQAGTTEVGDAIAAAKAAFPAWRDTDPRTRAEYLLKAAQAARKRLFELSAWQVLEIGKQWDQAYADVTEAIDFLEYYAREMIRLGQPQRVGHAPGELNHYFYEPKGVAAVIAPWNFPLAISMGMASAAIVTGNCVVFKPSGITSIIGWHLVELFREAGLPEGVFNFTPGRGSVMGDYLVDHPDISLIAFTGSMETGLRIIERAAKVHPGQANVKKIISEMGGKNAIIIDDDADLDEAVPHVLYSAFGFQGQKCSACSRVIVLDAVYDKFIERLVSMAKATKVGPSEDPANYMGAVADDKAMKSIKEYAEIGKREGHVLYESPVPAGEGYFVPMTIIGGIKPEHRIAQEEIFGPVLAVMRAKDFDQAIEWANSTQFALTGGIFSRSPEHLAKARREFRVGNLYINRNNTGALVERQPFGGARMSGVGTKAGGPDYLLHFMDPRVVTENTMRRGFAPIEEDDDWV 1003
                                    12        22        32        42        52        62        72        82     ||105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455  ||   477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      
                                                                                                                88|                                                                                                                                                                                                                                                                                                                                                                 458|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                102                                                                                                                                                                                                                                                                                                                                                                  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 4NMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4nm9 4nma 4nmc 4nmd 4nme 4nmf