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(-) Description

Title :  STRUCTURE OF A NITRATE/NITRITE ANTIPORTER NARK IN NITRATE-BOUND OCCLUDED STATE
 
Authors :  M. Fukuda, H. Takeda, H. E. Kato, S. Doki, K. Ito, A. D. Maturana, R. Ishit O. Nureki
Date :  24 Jul 14  (Deposition) - 15 Jul 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transporter, Nitrate Nitrite Porter Family, Major Facilitator Superfamily, Membrane Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fukuda, H. Takeda, H. E. Kato, S. Doki, K. Ito, A. D. Maturana, R. Ishitani, O. Nureki
Structural Basis For Dynamic Mechanism Of Nitrate/Nitrite Antiport By Nark
Nat Commun V. 6 7097 2015
PubMed-ID: 25959928  |  Reference-DOI: 10.1038/NCOMMS8097

(-) Compounds

Molecule 1 - NITRATE/NITRITE TRANSPORTER NARK
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET VARIANT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NARK, B1223, JW1214
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR. MG1655
    Organism Taxid: 511145
    Strain: MG1655
    Synonym: NITRITE EXTRUSION PROTEIN 1,NITRITE FACILITATOR 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1NO32Ligand/IonNITRATE ION
2OLA10Ligand/IonOLEIC ACID
3OLC5Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
2OLA5Ligand/IonOLEIC ACID
3OLC3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1NO31Ligand/IonNITRATE ION
2OLA5Ligand/IonOLEIC ACID
3OLC2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:49 , ARG A:89 , PHE A:147 , ASN A:175 , TYR A:263 , PHE A:267 , ARG A:305 , SER A:411binding site for residue NO3 A 501
02AC2SOFTWAREPRO A:91 , TYR A:92 , OLC A:509binding site for residue OLA A 502
03AC3SOFTWAREPRO A:43 , LEU A:47 , ILE A:218 , PHE A:222binding site for residue OLA A 503
04AC4SOFTWAREPHE A:121 , PHE A:197 , PRO A:221binding site for residue OLA A 504
05AC5SOFTWARELEU A:88 , SER A:131 , LEU A:138 , PHE A:142 , OLA B:502binding site for residue OLA A 505
06AC6SOFTWAREPHE A:420 , ALA A:424 , GLY A:437 , LYS B:203binding site for residue OLA A 506
07AC7SOFTWARELEU A:183 , GLN A:292binding site for residue OLC A 507
08AC8SOFTWAREPHE A:107 , GLY A:110 , ILE A:228 , TRP A:231 , PHE A:232 , OLC A:509 , ILE B:228 , PHE B:232binding site for residue OLC A 508
09AC9SOFTWAREILE A:98 , PHE A:99 , OLA A:502 , OLC A:508 , TRP B:39 , OLA B:505 , OLA B:506binding site for residue OLC A 509
10AD1SOFTWAREPHE B:49 , ARG B:89 , PHE B:147 , ASN B:175 , TYR B:263 , PHE B:267binding site for residue NO3 B 501
11AD2SOFTWAREILE A:135 , OLA A:505 , LEU B:187 , LEU B:191 , OLA B:503binding site for residue OLA B 502
12AD3SOFTWARELEU B:47 , TRP B:219 , PHE B:222 , OLA B:502binding site for residue OLA B 503
13AD4SOFTWAREPHE B:194 , PHE B:197 , TRP B:217binding site for residue OLA B 504
14AD5SOFTWAREOLC A:509 , SER B:35 , TRP B:39 , ALA B:166binding site for residue OLA B 505
15AD6SOFTWAREOLC A:509 , SER B:306binding site for residue OLA B 506
16AD7SOFTWAREILE A:111 , TRP A:118 , PHE A:121 , ASP A:125 , LEU A:139 , PHE A:142 , SER B:192 , ILE B:193 , PHE B:194 , ALA B:195 , VAL B:196 , ILE B:218 , PHE B:222 , ILE B:225 , HOH B:645binding site for residue OLC B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U4W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Thr A:341 -Asp A:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U4W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U4W)

(-) Exons   (0, 0)

(no "Exon" information available for 4U4W)

(-) Sequences/Alignments

Asymmetric 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:438
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............ee.....ee..hhhhhhhhhhhhhhhhhhhhhh.ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u4w A  11 TGAVITDWRPEDPAFWQQRGQRIASRNLWISVPCLLLAFCVWMLFSAVAVNLPKVGFNFTTDQLFMLTALPSVSGALLRVPYSFMVPIFGGRRWTAFSTGILIIPCVWLGFAVQDTSTPYSVFIIISLLCGFAGANFASSMANISFFFPKQKQGGALGLNGGLGNMGVSVMQLVAPLVVSLSIFAVFGSQGVKQPDGTELYLANASWIWVPFLAIFTIAAWFGMNDLATSKAKRGHLWIMSLLYLATFGSFIGFSAGFAMLSKTQFPDVQILQYAFFGPFIGALARSAGGALSDRLGGTRVTLVNFILMAIFSGLLFLTLPTDGQGGSFMAFFAVFLALFLTAGLGSGSTFQMISVIFRKLTMDRVKAEGGSDERAMREAATDTAAALGFISAIGAIGGFFIPKAFGSSLALTGSPVGAMKVFLIFYIACVVITWAVY 457
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 ||    259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449        
                                                                                                                                                                                                                                                                 242|                                                                                                                                                                                                             
                                                                                                                                                                                                                                                                  252                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh............ee.....ee..hhhhhhhhhhhhhhhhhhhhhh.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u4w B  12 GAVITDWRPEDPAFWQQRGQRIASRNLWISVPCLLLAFCVWMLFSAVAVNLPKVGFNFTTDQLFMLTALPSVSGALLRVPYSFMVPIFGGRRWTAFSTGILIIPCVWLGFAVQDTSTPYSVFIIISLLCGFAGANFASSMANISFFFPKQKQGGALGLNGGLGNMGVSVMQLVAPLVVSLSIFAVFGSQGVKQPDGTELYLANASWIWVPFLAIFTIAAWFGMNDLARGHLWIMSLLYLATFGSFIGFSAGFAMLSKTQFPDVQILQYAFFGPFIGALARSAGGALSDRLGGTRVTLVNFILMAIFSGLLFLTLPQGGSFMAFFAVFLALFLTAGLGSGSTFQMISVIFRKLTMDRVKAEGGSDERAMREAATDTAAALGFISAIGAIGGFFIPKAFGSSLALTGSPVGAMKVFLIFYIACVVITWAVYG 458
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      |255       265       275       285       295       305       315       325       335    || 348       358       368       378       388       398       408       418       428       438       448       458
                                                                                                                                                                                                                                                            238|                                                                                    340|                                                                                                                  
                                                                                                                                                                                                                                                             253                                                                                     344
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4U4W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U4W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U4W)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        NARK_ECOLI | P10903: 4jr9 4jre 4u4t 4u4v

(-) Related Entries Specified in the PDB File

4u4t 4u4v