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Title :   STRUCTURE OF APO FORM OF A PERIPLASMIC HEME BINDING PROTEIN

Authors :   D. Mattle, B. A. Goetz, K. P. Locher

Date :   30 Mar 10 (Deposition) - 15 Sep 10 (Release) - 23 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Transport Protein, Alpha Beta Protein, Rigid Helical Backbone, Substrate-Free, Heme Transport, Iron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Mattle, A. Zeltina, J. S. Woo, B. A. Goetz, K. P. Locher
Two Stacked Heme Molecules In The Binding Pocket Of The Periplasmic Heme-Binding Protein Hmut From Yersinia Pestis.
J. Mol. Biol. V. 404 220 2010
PubMed-ID: 20888343 | Reference-DOI: 10.1016/J.JMB.2010.09.005

Molecule 1 - HEMIN-BINDING PERIPLASMIC PROTEIN HMUT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HMUT, YPO0281, Y0541, YP_0436
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		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 (3, 9)

No.	Name	Count	Type	Full Name
1	BR	7	Ligand/Ion	BROMIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BR	-1	Ligand/Ion	BROMIDE ION
2	GOL	-1	Ligand/Ion	GLYCEROL
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:181 , TYR A:200	BINDING SITE FOR RESIDUE BR A 401
2	AC2	SOFTWARE	ARG A:72	BINDING SITE FOR RESIDUE BR A 402
3	AC3	SOFTWARE	LEU A:249 , LYS A:274 , HOH A:491 , HOH B:3	BINDING SITE FOR RESIDUE BR A 403
4	AC4	SOFTWARE	ARG A:201 , PRO A:202 , SER A:204 , GLY A:207 , VAL A:208 , HOH A:313 , HOH A:368	BINDING SITE FOR RESIDUE GOL A 600
5	AC5	SOFTWARE	HOH A:9 , LEU B:249 , LYS B:274 , HOH B:423	BINDING SITE FOR RESIDUE BR B 401
6	AC6	SOFTWARE	MET B:194 , SER B:204 , HOH B:495	BINDING SITE FOR RESIDUE BR B 402
7	AC7	SOFTWARE	ARG B:72	BINDING SITE FOR RESIDUE BR B 403
8	AC8	SOFTWARE	HOH B:1 , THR B:179 , ALA B:180 , ARG B:199 , HOH B:343 , HOH B:371 , HOH B:437	BINDING SITE FOR RESIDUE SO4 B 500

(no "SS Bond" information available for 3MD9)

Asymmetric Unit

No.	Residues
1	Gln A:58	-	Pro A:59
2	Gln A:94	-	Pro A:95
3	Gln B:58	-	Pro B:59
4	Gln B:94	-	Pro B:95

(no "SAP(SNP)/Variant" information available for 3MD9)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	HMUT_YERPE	28-279	2	A:28-278 B:28-278

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	HMUT_YERPE	28-279	1	A:28-278 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FE_B12_PBP	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.	HMUT_YERPE	28-279	1	- B:28-278

(no "Exon" information available for 3MD9)

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
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Chain A from PDB  Type:PROTEIN  Length:253
 aligned with HMUT_YERPE | Q56991 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:253
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275   
           HMUT_YERPE    26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQM 278
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee......hhhhhhh.........hhhhhhh....eeeee....hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee.......eee...hhhhhhhhhh..ee.......eee.hhhhhhhhh..eeeeehhhhhhhhhhhhhhhh.hhhhhhhhhh..eeeehhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: A:28-278 UniProt: 28-279                                                                                                                                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3md9 A  26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQM 278
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with HMUT_YERPE | Q56991 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:253
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275   
           HMUT_YERPE    26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQM 278
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Peripla_BP_2-3md9B01 B:29-256                                                                                                                                                                                                       ---------------------- Pfam domains (1)
           Pfam domains (2) ---Peripla_BP_2-3md9B02 B:29-256                                                                                                                                                                                                       ---------------------- Pfam domains (2)
         Sec.struct. author ...eeeehhhhhhhhhhh.hhh.eeee......hhhhhhh....hhhhhhhhhhhh....eeeee....hhhhhhhhhhh..eeeee.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh........eeeeeeee..eeeeee...hhhhhhhhhh..ee.......eee.hhhhhhhhh..eeeeehhhhhhhh.hhhhhhh.hhhhhhhhhhh.eeeehhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --FE_B12_PBP  PDB: B:28-278 UniProt: 28-279                                                                                                                                                                                                                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3md9 B  26 AERIVTIGGDVTEIAYALGAGDEIVARDSTSQQPQAAQKLPDVGYMRTLNAEGILAMKPTMLLVSELAQPSLVLTQIASSGVNVVTVPGQTTPESVAMKINAVATALHQTEKGQKLIEDYQQRLAAVNKTPLPVKVLFVMSHGGLTPMAAGQNTAADAMIRAAGGSNAMQGFSRYRPLSQEGVIASAPDLLLITTDGVKALGSSENIWKLPGMALTPAGKHKRLLVVDDMALLGFGLETPQVLAQLREKMEQM 278
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

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 '\|'

(no "SCOP Domain" information available for 3MD9)

(no "CATH Domain" information available for 3MD9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Peripla_BP_2] (13)

Family: Peripla_BP_2 (13)

Yersinia pestis (1)

1a	Peripla_BP_2-3md9B01	B:29-256
1b	Peripla_BP_2-3md9B02	B:29-256

Asymmetric Unit(hide GO term definitions)

Chain A,B (HMUT_YERPE | Q56991)

molecular function
	GO:0036094	small molecule binding	Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
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:0055072	iron ion homeostasis	Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
	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:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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		Gln B:94 - Pro B:95	[ RasMol ]

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3md8	STRUCTURE OF A PERIPLASMIC HEME BINDING PROTEIN
3nu1	STRUCTURE OF HOLO FORM OF A PERIPLASMIC HEME BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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Exons (0, 0)

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