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Title :   STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN COMPLEX WITH INDIUM-PORPHYRIN

Authors :   N. T. Vu, J. M. M. Caaveiro, Y. Moriwaki, K. Tsumoto

Date :   31 May 12 (Deposition) - 15 May 13 (Release) - 21 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Indium, Metalloporphyrin, Metal Selectivity, Neat Domain, Heme Binding, Heme Transport, Hemin, Ppix, Cell Wall, Heme-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. T. Vu, Y. Moriwaki, J. M. M. Caaveiro, T. Terada, H. Tsutsumi, I. Hamachi, K. Shimizu, K. Tsumoto
Selective Binding Of Antimicrobial Porphyrins To The Heme-Receptor Isdh-Neat3 Of Staphylococcus Aureus
Protein Sci. V. 22 942 2013
PubMed-ID: 23649633 | Reference-DOI: 10.1002/PRO.2276
(for further references see the PDB file header)

Molecule 1 - IRON-REGULATED SURFACE DETERMINANT PROTEIN H
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA2(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NEAT DOMAIN, UNP RESIDUES 543-655
	Gene	:	HARA, ISDH, ISDH-NEAT3, SASI, SAV1731
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	158878
	Strain	:	STRAIN MU50 / ATCC 700699
	Synonym	:	HAPTOGLOBIN RECEPTOR A, STAPHYLOCOCCUS AUREUS SURFACE PROTEIN I

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	3ZZ	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING INDIUM
2	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	3ZZ	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING INDIUM
2	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	3ZZ	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING INDIUM
2	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:556 , SER A:563 , VAL A:564 , PHE A:568 , TRP A:594 , VAL A:635 , TYR A:642 , TYR A:646 , VAL A:648 , VAL B:564 , 3ZZ B:701	BINDING SITE FOR RESIDUE 3ZZ A 701
2	AC2	SOFTWARE	TRP A:594 , ASP A:596 , LEU A:597 , THR A:606 , ARG A:616 , HOH A:805	BINDING SITE FOR RESIDUE GOL A 702
3	AC3	SOFTWARE	VAL A:564 , 3ZZ A:701 , SER B:563 , VAL B:564 , PHE B:568 , TYR B:593 , TRP B:594 , VAL B:635 , ILE B:640 , TYR B:642 , TYR B:646 , VAL B:648	BINDING SITE FOR RESIDUE 3ZZ B 701
4	AC4	SOFTWARE	ASP B:591 , TRP B:594 , LYS B:595 , ASP B:596 , LEU B:597 , ARG B:616 , LEU B:618	BINDING SITE FOR RESIDUE GOL B 702

(no "SS Bond" information available for 3VTM)

Asymmetric Unit

No.	Residues
1	His A:571	-	Pro A:572
2	His B:571	-	Pro B:572

(no "SAP(SNP)/Variant" information available for 3VTM)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	2	- - A:543-655 B:543-655

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	1	- - A:543-655 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NEAT	PS50978	NEAT domain profile.	ISDH_STAAM	105-232 345-471 543-660	1	- - - B:543-655

(no "Exon" information available for 3VTM)

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:113
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:113
                                   552       562       572       582       592       602       612       622       632       642       652   
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d3vtma_ A: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eeeee.......hhhhhh...eeeeee..eeeeeee..hhh.eeeeee..ee.eeeeeehhhheeeeeee......eeeeeeeeeehhhheeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: A:543-655 UniProt: 543-660                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3vtm A 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
                                   552       562       572       582       592       602       612       622       632       642       652

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with ISDH_STAAM | Q931P4 from UniProtKB/Swiss-Prot  Length:891

    Alignment length:113
                                   552       562       572       582       592       602       612       622       632       642       652   
           ISDH_STAAM   543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
               SCOP domains d3vtmb_ B: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.eeee.......hhhhhhh...eeeeee..eeeeeee......eeeeee..ee.eeeeee....eeeeeee......eeeeeeeeeehhhheeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NEAT  PDB: B:543-655 UniProt: 543-660                                                                             PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3vtm B 543 QLTDLQEAHFVVFESEENSESVMDGFVEHPFYTATLNGQKYVVMKTKDDSYWKDLIVEGKRVTTVSKDPKNNSRTLIFPYIPDKAVYNAIVKVVVANIGYEGQYHVRIINQDI 655
                                   552       562       572       582       592       602       612       622       632       642       652

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

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Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: NEAT domain-like (27)

Family: automated matches (13)

Protein domain: automated matches (13)

Staphylococcus aureus [TaxId: 158879] (7)

1a	d3vtma_	A:
1b	d3vtmb_	B:

(no "CATH Domain" information available for 3VTM)

(no "Pfam Domain" information available for 3VTM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ISDH_STAAM | Q931P4)


GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	ISDH_STAAM \| Q931P4	:	2e7d 2z6f 3qug 3quh 3vua

2e7d	CRYSTAL STRUCTURE OF A NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS
2z6f	CRYSTAL STRUCTURE OF NEAT DOMAIN FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH HEME
3qug	STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN COMPLEX WITH GALLIUM-PORPHYRIN
3quh	STRUCTURE OF HEME TRANSPORT PROTEIN ISDH-NEAT3 FROM S. AUREUS IN COMPLEX WITH MANGANESE(III)-PORPHYRIN

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