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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3RD PDZ DOMAIN OF INTESTINE- AND KIDNEY-ENRICHED PDZ DOMAIN IKEPP (PDZD3)
 
Authors :  J. Uppenberg, C. Gileadi, C. Phillips, J. Elkins, G. Bunkoczi, C. Coope A. C. W. Pike, E. Salah, E. Ugochukwu, C. H. Arrowsmith, A. Edwards, M. S J. Weigelt, D. A. Doyle
Date :  16 Aug 07  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Pdzd3, Membrane, Pdz Domain, Protein-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Uppenberg, C. Gileadi, C. Phillips, J. Elkins, G. Bunkoczi, C. Cooper, A. C. W. Pike, E. Salah, E. Ugochukwu, C. H. Arrowsmith, A. Edwards, M. Sundstrom, J. Weigelt, D. A. Doyle
Crystal Structure Of The 3Rd Pdz Domain Of Intestine- And Kidney-Enriched Pdz Domain Ikepp ( Pdzd3)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PDZ DOMAIN-CONTAINING PROTEIN 3
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: DE3-R3
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN, RESIDUES 246-335
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PDZ DOMAIN-CONTAINING PROTEIN 2, INTESTINAL AND KIDNEY-ENRICHED PDZ PROTEIN, INTESTINE- AND KIDNEY-ENRICHED PDZ DOMAIN IKEPP

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:268 , LEU A:269 , ASP A:270 , HOH A:2073 , HOH A:2074BINDING SITE FOR RESIDUE SO4 A1340
2AC2SOFTWAREGLY B:268 , LEU B:269 , ASP B:270 , SO4 B:1341 , HOH B:2063 , HOH B:2064BINDING SITE FOR RESIDUE SO4 B1340
3AC3SOFTWAREGLY B:268 , ARG B:296 , SO4 B:1340 , HOH B:2065BINDING SITE FOR RESIDUE SO4 B1341

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V90)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.NHRF4_HUMAN115-196
223-301
329-412
 
 
 
 
 
467-548		  6-
-
A:249-332
B:249-332
C:249-332
D:249-332
E:249-332
F:249-332
-

(-) Exons   (0, 0)

(no "Exon" information available for 2V90)

(-) 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:95
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:134
                                   334       344       354       364       374       384       394       404       414       424       434       444       454    
          NHRF4_HUMAN   325 TKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90a_ A: automated matches                                                                                                           SCOP domains
               CATH domains 2v90A00 A:245-339  [code=2.30.42.10, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeeee.....eeeeeeee...hhhhhh.....eeeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v90 A 245 MKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   254       264       274       284       294       304       314       324       334|        -         -         -         -|   
                                                                                                                    335                                     336   


Chain B from PDB  Type:PROTEIN  Length:95
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:134
                                   334       344       354       364       374       384       394       404       414       424       434       444       454    
          NHRF4_HUMAN   325 TKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90b_ B: automated matches                                                                                                           SCOP domains
               CATH domains 2v90B00 B:245-339  [code=2.30.42.10, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeeee.....eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v90 B 245 MKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   254       264       274       284       294       304       314       324       334|        -         -         -         -|   
                                                                                                                    335                                     336   


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:132
                                   336       346       356       366       376       386       396       406       416       426       436       446       456  
          NHRF4_HUMAN   327 PRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90c_ C: automated matches                                                                                                         SCOP domains
               CATH domains 2v90C00 C:247-339  [code=2.30.42.10, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......eeeeeee.....eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --PDZ  PDB: C:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v90 C 247 PRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   256       266       276       286       296       306       316       326        |-         -         -         -       337  
                                                                                                                  335                                     336   


Chain D from PDB  Type:PROTEIN  Length:93
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:132
                                   336       346       356       366       376       386       396       406       416       426       436       446       456  
          NHRF4_HUMAN   327 PRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90d_ D: automated matches                                                                                                         SCOP domains
               CATH domains 2v90D00 D:247-339  [code=2.30.42.10, no name defined]                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.......eeeeeee.....eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --PDZ  PDB: D:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2v90 D 247 PRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   256       266       276       286       296       306       316       326        |-         -         -         -       337  
                                                                                                                  335                                     336   


Chain E from PDB  Type:PROTEIN  Length:95
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:134
                                   334       344       354       364       374       384       394       404       414       424       434       444       454    
          NHRF4_HUMAN   325 TKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90e_ E: automated matches                                                                                                           SCOP domains
               CATH domains 2v90E00 E:245-339  [code=2.30.42.10, no name defined]                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......eeeeeee.....eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: E:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v90 E 245 MKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   254       264       274       284       294       304       314       324       334|        -         -         -         -|   
                                                                                                                    335                                     336   


Chain F from PDB  Type:PROTEIN  Length:95
 aligned with NHRF4_HUMAN | Q86UT5 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:134
                                   334       344       354       364       374       384       394       404       414       424       434       444       454    
          NHRF4_HUMAN   325 TKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADRFFSMVRLSPLLFLENTEAPASPRGSSSASLVETEDPSLEDTSV 458
               SCOP domains d2v90f_ F: automated matches                                                                                                           SCOP domains
               CATH domains 2v90F00 F:245-339  [code=2.30.42.10, no name defined]                                                                                  CATH domains
           Pfam domains (1) -----PDZ-2v90F01 F:250-329                                                           ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----PDZ-2v90F02 F:250-329                                                           ------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----PDZ-2v90F03 F:250-329                                                           ------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----PDZ-2v90F04 F:250-329                                                           ------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -----PDZ-2v90F05 F:250-329                                                           ------------------------------------------------- Pfam domains (5)
           Pfam domains (6) -----PDZ-2v90F06 F:250-329                                                           ------------------------------------------------- Pfam domains (6)
         Sec.struct. author ...eeeeee.......eeeeeee.....eeeeeeee...hhhhhh......eeeee..ee....hhhhhhhhhhh...eeeeeee......---------------------------------------eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: F:249-332 UniProt: 329-412                                                ---------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v90 F 245 MKPRCLHLEKGPQGFGFLLREEKGLDGRPGQFLWEVDPGLPAKKAGMQAGDRLVAVAGESVEGLGHEETVSRIQGQGSCVSLTVVDPEADR---------------------------------------ETSV 339
                                   254       264       274       284       294       304       314       324       334|        -         -         -         -|   
                                                                                                                    335                                     336
   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  (1, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Roll (1513)
(-)
Topology: Pdz3 Domain (191)
(-)
Homologous Superfamily: [code=2.30.42.10, no name defined] (191)
(-)
Human (Homo sapiens) (120)
1a2v90A00A:245-339
1b2v90B00B:245-339
1c2v90E00E:245-339
1d2v90F00F:245-339
1e2v90C00C:247-339
1f2v90D00D:247-339

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
(-)
Homo sapiens (Human) (96)
1aPDZ-2v90F01F:250-329
1bPDZ-2v90F02F:250-329
1cPDZ-2v90F03F:250-329
1dPDZ-2v90F04F:250-329
1ePDZ-2v90F05F:250-329
1fPDZ-2v90F06F:250-329

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (NHRF4_HUMAN | Q86UT5)
molecular function
    GO:0030251    guanylate cyclase inhibitor activity    Stops, prevents or reduces the activity of guanylate cyclase.
    GO:0008200    ion channel inhibitor activity    Stops, prevents, or reduces the activity of an ion channel.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019934    cGMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic GMP (cGMP). Includes production of cGMP, and downstream effectors that further transmit the signal within the cell.
    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:0030827    negative regulation of cGMP biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of cGMP.
    GO:0031283    negative regulation of guanylate cyclase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of guanylate cyclase activity.
    GO:0007168    receptor guanylyl cyclase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses guanylyl cyclase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0006833    water transport    The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
    GO:0045177    apical part of cell    The region of a polarized cell that forms a tip or is distal to a base. For example, in a polarized epithelial cell, the apical region has an exposed surface and lies opposite to the basal lamina that separates the epithelium from other tissue.
    GO:0005903    brush border    The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0035003    subapical complex    The most apical region of the lateral plasma membrane of an invertebrate epithelial cell. The subapical complex lies above the zonula adherens and the septate junction, and is comparable to the position of the tight junction of vertebrate cells.

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