2R4H - JenaLib

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Title :   CRYSTAL STRUCTURE OF A C1190S MUTANT OF THE 6TH PDZ DOMAIN OF HUMAN MEMBRANE ASSOCIATED GUANYLATE KINASE

Authors :   E. Ugochukwu, E. S. Pilka, V. Hozjan, K. L. Kavanagh, C. Cooper, A. C. W. P J. M. Elkins, D. A. Doyle, F. Von Delft, M. Sundstrom, C. H. Arrowsmith J. Weigelt, A. M. Edwards, U. Oppermann, Structural Genomics Conso (Sgc)

Date :   31 Aug 07 (Deposition) - 16 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Transferase, Pdz, Membrane Associated Guanylate Kinase, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Cell Junction, Nucleotide-Binding, Phosphorylation, Tight Junction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Ugochukwu, E. S. Pilka, V. Hozjan, K. L. Kavanagh, C. Cooper, A. C. W. Pike, J. M. Elkins, D. A. Doyle, F. Von Delft, M. Sundstrom, C. H. Arrowsmith, J. Weigelt, A. M. Edwards, U. Oppermann
Crystal Structure Of A C1190S Mutant Of The 6Th Pdz Domain Of Human Membrane Associated Guanylate Kinase.
To Be Published
PubMed: search

Molecule 1 - MEMBRANE-ASSOCIATED GUANYLATE KINASE, WW AND PDZ DOMAIN- CONTAINING PROTEIN 1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3-PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	6TH PDZ DOMAIN: RESIDUES 1149-1233
	Gene	:	MAGI1, BAIAP1, BAP1, TNRC19
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BAI1-ASSOCIATED PROTEIN 1, BAP-1, MEMBRANE-ASSOCIATED GUANYLATE KINASE INVERTED 1, MAGI-1, ATROPHIN-1-INTERACTING PROTEIN 3, AIP3, WW DOMAIN-CONTAINING PROTEIN 3, WWP3, TRINUCLEOTIDE REPEAT- CONTAINING GENE 19 PROTEIN
	Tissue	:	BRAIN

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	HIS	5	Mod. Amino Acid	HISTIDINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HIS	2	Mod. Amino Acid	HISTIDINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	HIS	-1	Mod. Amino Acid	HISTIDINE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	HIS	3	Mod. Amino Acid	HISTIDINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:47 , ILE A:48 , HIS A:92 , HOH A:116 , HIS C:93	BINDING SITE FOR RESIDUE HIS A 91
2	AC2	SOFTWARE	ARG A:47 , HIS A:91 , HIS C:93	BINDING SITE FOR RESIDUE HIS A 92
3	AC3	SOFTWARE	ASN C:26 , MET C:27 , ASP C:28 , HIS C:92	BINDING SITE FOR RESIDUE HIS C 91
4	AC4	SOFTWARE	GLU C:51 , HIS C:91 , HIS C:93	BINDING SITE FOR RESIDUE HIS C 92
5	AC5	SOFTWARE	HIS A:91 , HIS A:92 , TYR C:30 , HIS C:92 , HOH C:107 , HOH C:124 , HOH C:127	BINDING SITE FOR RESIDUE HIS C 93

(no "SS Bond" information available for 2R4H)

(no "Cis Peptide Bond" information available for 2R4H)

(no "SAP(SNP)/Variant" information available for 2R4H)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAGI1_HUMAN	17-105 472-541 643-721 841-923 998-1094 1152-1234	3	- - - - - A:5-86 B:5-86 C:5-86

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAGI1_HUMAN	17-105 472-541 643-721 841-923 998-1094 1152-1234	1	- - - - - A:5-86 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAGI1_HUMAN	17-105 472-541 643-721 841-923 998-1094 1152-1234	1	- - - - - - B:5-86 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	MAGI1_HUMAN	17-105 472-541 643-721 841-923 998-1094 1152-1234	1	- - - - - - - C:5-86

(no "Exon" information available for 2R4H)

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:92
 aligned with MAGI1_HUMAN | Q96QZ7 from UniProtKB/Swiss-Prot  Length:1491

    Alignment length:92
                                  1157      1167      1177      1187      1197      1207      1217      1227      1237  
         MAGI1_HUMAN   1148 QDFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERCGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGDGSVPE 1239
               SCOP domains d2r4ha_ A: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeee.hhhh..eeeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhh...eeeeeee..eee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:5-86 UniProt: 1152-1234                                                ----- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                2r4h A    1 MDFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERSGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGETSVHH   92
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:89
 aligned with MAGI1_HUMAN | Q96QZ7 from UniProtKB/Swiss-Prot  Length:1491

    Alignment length:89
                                  1158      1168      1178      1188      1198      1208      1218      1228         
         MAGI1_HUMAN   1149 DFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERCGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGDGSV 1237
               SCOP domains d2r4hb_ B: automated matches                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeeehhhheeeeeeee...hhhhhh.......eeeee..ee....hhhhhhhhhhhh..eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---PDZ  PDB: B:5-86 UniProt: 1152-1234                                                --- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                2r4h B    2 DFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERSGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGETSV   90
                                    11        21        31        41        51        61        71        81

Chain C from PDB  Type:PROTEIN  Length:101
 aligned with MAGI1_HUMAN | Q96QZ7 from UniProtKB/Swiss-Prot  Length:1491

    Alignment length:116
                                  1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      
         MAGI1_HUMAN   1125 TRNTTKPKQESQFEFKAPQATQEQDFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERCGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGDGSVPEY 1240
               SCOP domains d2r         4hc_       C: automated matches                                                                          SCOP domains
               CATH domains ----------------2      r4hC01 C:0-87  [code=2.30.42.10, no name defined]                                      ------ CATH domains
           Pfam domains (1) ---------------------------PDZ-2r4hC01 C:5-84                                                              --------- Pfam domains (1)
           Pfam domains (2) ---------------------------PDZ-2r4hC02 C:5-84                                                              --------- Pfam domains (2)
           Pfam domains (3) ---------------------------PDZ-2r4hC03 C:5-84                                                              --------- Pfam domains (3)
         Sec.struct. author hhh---------hhhhh------hheeeeeee.......eeeeeehhhheeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------PDZ  PDB: C:5-86 UniProt: 1152-1234                                                ------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                2r4h C   -7 TEN---------LYFQS------MDFYTVELERGAKGFGFSLRGGREYNMDLYVLRLAEDGPAERSGKMRIGDEILEINGETTKNMKHSRAIELIKNGGRRVRLFLKRGETSVHHH   93
                              |      -  |   |  -   |     7        17        27        37        47        57        67        77        87      
                             -5        -4   0      1

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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d2r4ha_	A:
1b	d2r4hb_	B:
1c	d2r4hc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

2r4hC01

C:0-87

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ (172)

Homo sapiens (Human) (96)

1a	PDZ-2r4hC01	C:5-84
1b	PDZ-2r4hC02	C:5-84
1c	PDZ-2r4hC03	C:5-84

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (MAGI1_HUMAN | Q96QZ7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0051393	alpha-actinin binding	Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats.
	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: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).
	GO:0032947	protein complex scaffold activity	A structural molecule activity that provides a physical support for the assembly of a multiprotein complex. The scaffold may or may not be part of the final complex.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	GO:0070997	neuron death	The process of cell death in a neuron.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
cellular component
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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	2r4h
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	MAGI1_HUMAN \| Q96QZ7	:	1wbp 2kpk 2kpl 2q9v 2ysd 2yse 2zaj 3bpu

2q9v	CRYSTAL STRUCTURE OF THE C890S MUTANT OF THE 4TH PDZ DOMAIN OF HUMAN MEMBRANE ASSOCIATED GUANYLATE KINASE

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