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(-) Description

Title :  STRUCTURE AND FUNCTION OF THE PORB PORIN FROM DISSEMINATING N. GONORRHOEAE
 
Authors :  K. Zeth, V. Kozjak-Pavlovic, M. Faulstich, R. Hurwitz, O. Kepp, T. Rude
Date :  17 May 12  (Deposition) - 10 Oct 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  F  (1x)
Keywords :  Membrane Protein, Outer Membrane Protein, Infection, Invasion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Zeth, V. Kozjak-Pavlovic, M. Faulstich, M. Fraunholz, R. Hurwitz, O. Kepp, T. Rudel
Structure And Function Of The Porb Porin From Disseminating Neisseria Gonorrhoeae.
Biochem. J. V. 449 631 2013
PubMed-ID: 23095086  |  Reference-DOI: 10.1042/BJ20121025

(-) Compounds

Molecule 1 - PORIN (PORB)
    Chains: A, B, C
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 485
 
Molecule 2 - POLY ALA
    Chains: D, E, F
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    D  
Biological Unit 3 (1x):     E 
Biological Unit 4 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ATP3Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO46Ligand/IonPHOSPHATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ATP-1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3PO4-1Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:9 , GLY A:38 , LYS A:40 , GLU A:60 , LYS A:62 , ARG A:75 , LYS A:98 , ARG A:124 , MG A:403BINDING SITE FOR RESIDUE ATP A 400
02AC2SOFTWAREILE A:96 , ASP A:99 , ARG A:129 , SER A:141 , ASN A:163BINDING SITE FOR RESIDUE PO4 A 401
03AC3SOFTWAREASN A:74 , ARG A:92 , ARG A:124BINDING SITE FOR RESIDUE PO4 A 402
04AC4SOFTWARELYS A:9 , GLU A:107 , ATP A:400BINDING SITE FOR RESIDUE MG A 403
05AC5SOFTWARELYS B:9 , GLY B:38 , LYS B:40 , GLN B:58 , GLU B:60 , ARG B:75 , GLN B:76 , ARG B:124 , LYS B:307BINDING SITE FOR RESIDUE ATP B 400
06AC6SOFTWAREILE B:96 , ASP B:99 , THR B:100 , SER B:141 , PHE B:162 , ASN B:163 , TYR B:173BINDING SITE FOR RESIDUE PO4 B 401
07AC7SOFTWARELYS B:62 , ASN B:74 , ARG B:92 , ARG B:124BINDING SITE FOR RESIDUE PO4 B 402
08AC8SOFTWARELYS C:9 , GLY C:38 , LYS C:40 , GLN C:58 , GLU C:60 , ARG C:75 , GLN C:76 , ASN C:94 , LYS C:98 , ARG C:124BINDING SITE FOR RESIDUE ATP C 400
09AC9SOFTWAREILE C:96 , ASP C:99 , THR C:100 , SER C:141 , ASN C:163BINDING SITE FOR RESIDUE PO4 C 401
10BC1SOFTWAREASN C:74 , ARG C:92 , ARG C:124BINDING SITE FOR RESIDUE PO4 C 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (21, 21)

Asymmetric Unit
No.Residues
1His A:20 -His A:21
2Leu A:49 -Gly A:50
3Gly A:114 -Leu A:115
4Asn A:147 -Asp A:148
5Ser A:150 -Gly A:151
6Asp A:219 -Asn A:220
7Leu B:49 -Gly B:50
8Gly B:114 -Leu B:115
9Asn B:147 -Asp B:148
10Ser B:150 -Gly B:151
11Asp B:219 -Asn B:220
12Leu C:49 -Gly C:50
13Gly C:114 -Leu C:115
14Asn C:147 -Asp C:148
15Ser C:150 -Gly C:151
16Asp C:219 -Asn C:220
17Ala D:400 -Ala D:401
18Ala D:401 -Ala D:402
19Ala D:404 -Ala D:405
20Ala E:401 -Ala E:402
21Ala F:404 -Ala F:405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AUI)

(-) 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:308
 aligned with Q51056_NEIGO | Q51056 from UniProtKB/TrEMBL  Length:327

    Alignment length:308
                                    29        39        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        
         Q51056_NEIGO    20 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGGFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNSGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 327
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeeeee..................eeeeeeee......eeeeeeeee...............eeeeee..eeeeeeeee.............................eeeeeeeeeeee..eeeeeeee...........eeeeeeeee...eeeeeeeeee......eeeeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeee.............eeeeeeeeeee....eeeeeeeeeeeee...eeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aui A   1 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGNFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNDGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        


Chain B from PDB  Type:PROTEIN  Length:308
 aligned with Q51056_NEIGO | Q51056 from UniProtKB/TrEMBL  Length:327

    Alignment length:308
                                    29        39        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        
         Q51056_NEIGO    20 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGGFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNSGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 327
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeee....................eeeeeeee......eeeeeeeee...............eeeee....eeeeeeeehhhhhhh......................eeeeeeeeeeee..eeeeeeee...........eeeeeeeee...eeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeee.............eeeeeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aui B   1 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGNFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNDGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with Q51056_NEIGO | Q51056 from UniProtKB/TrEMBL  Length:327

    Alignment length:308
                                    29        39        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        
         Q51056_NEIGO    20 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGGFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNSGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 327
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeeee....................eeeeeeee......eeeeeeeee...............eeeee....eeeeeeee.............................eeeeeeeeeeee..eeeeeeee...........eeeeeeeee...eeeeeeeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeee.............eeeeeeeeeee....eeeeeeeeeeeee....eeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aui C   1 DVTLYGTIKAGVETSRSVAHHGAQADRVKTATEIADLGSKIGFKGQEDLGNGLKAIWQLEQKAYVSGTDTGWGNRQSFIGLKGGFGKVRVGRLNNILKDTGNFNPWEGKSYYSGLSNIAQPEERHVSVRYDSPEFAGFSGSVQYVPNDNSGKNRSESYHAGFNYKNDGFFVQYAGSYKRHNYTTEKHQVHRLVGGYDHDALYASVAVQQQDAKLTWRDDNSHNSQTEVATTVAYRFGNVTPRVSYAHGFKGSVYDADHDNTYDQVVVGAEYDFSKRTSALVSAGWLQKGKGAEKFVATVGGVGLRHKF 308
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300        


Chain D from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4aui D 400 AAAAAAAA 407


Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4aui E 401 AAAAAAAA 408


Chain F from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4aui F 402 AAAAAAA 408
   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 4AUI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q51056_NEIGO | Q51056)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0015288    porin activity    Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009279    cell outer membrane    A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0046930    pore complex    Any small opening in a membrane that allows the passage of gases and/or liquids.

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  Cis Peptide Bonds
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    Ala D:401 - Ala D:402   [ RasMol ]  
    Ala D:404 - Ala D:405   [ RasMol ]  
    Ala E:401 - Ala E:402   [ RasMol ]  
    Ala F:404 - Ala F:405   [ RasMol ]  
    Asn A:147 - Asp A:148   [ RasMol ]  
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  Q51056_NEIGO | Q51056
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