3ZJM - JenaLib

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Title :   ILE(149)G11PHE MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE

Authors :   A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Cole L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini

Date :   18 Jan 13 (Deposition) - 26 Jun 13 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Iron-Binding Protein, Haem-Distal Site Mutation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Pesce, L. Tilleman, J. Donne, E. Aste, P. Ascenzi, C. Ciaccio, M. Coletta, L. Moens, C. Viappiani, S. Dewilde, M. Bolognesi, M. Nardini
Structure And Haem-Distal Site Plasticity In Methanosarcina Acetivorans Protoglobin.
Plos One V. 8 66144 2013
PubMed-ID: 23776624 | Reference-DOI: 10.1371/JOURNAL.PONE.0066144

Molecule 1 - PROTOGLOBIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	METHANOSARCINA ACETIVORANS
	Organism Taxid	:	2214

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 11)

No.	Name	Count	Type	Full Name
1	CYN	3	Ligand/Ion	CYANIDE ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3	GOL	3	Ligand/Ion	GLYCEROL
4	HEM	3	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	CYN	2	Ligand/Ion	CYANIDE ION
2	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3	GOL	4	Ligand/Ion	GLYCEROL
4	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (4, 6)

No.	Name	Count	Type	Full Name
1	CYN	2	Ligand/Ion	CYANIDE ION
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:70 , TYR A:73 , PHE A:74 , TYR A:85 , VAL A:89 , ARG A:92 , PHE A:93 , TRP A:96 , TYR A:112 , ILE A:116 , ARG A:119 , HIS A:120 , LYS A:125 , ASN A:126 , ILE A:137 , TYR A:141 , LEU A:142 , PHE A:145 , ILE A:146 , VAL A:182 , TRP A:185 , CYN A:201 , HOH A:2084 , HOH A:2085 , HOH A:2108 , HOH A:2112	BINDING SITE FOR RESIDUE HEM A 200
02	AC2	SOFTWARE	TRP A:60 , TYR A:61 , PHE A:93 , HEM A:200	BINDING SITE FOR RESIDUE CYN A 201
03	AC3	SOFTWARE	LEU B:70 , TYR B:73 , PHE B:74 , TYR B:85 , VAL B:89 , ARG B:92 , PHE B:93 , TRP B:96 , TYR B:112 , ARG B:119 , HIS B:120 , LYS B:125 , ASN B:126 , ILE B:137 , TYR B:141 , LEU B:142 , PHE B:145 , ILE B:146 , VAL B:182 , TRP B:185 , CYN B:201 , HOH B:2112 , HOH B:2113 , HOH B:2141 , HOH B:2145	BINDING SITE FOR RESIDUE HEM B 200
04	AC4	SOFTWARE	TRP B:60 , TYR B:61 , PHE B:93 , HEM B:200	BINDING SITE FOR RESIDUE CYN B 201
05	AC5	SOFTWARE	LEU C:70 , TYR C:73 , PHE C:74 , TYR C:85 , VAL C:89 , ARG C:92 , PHE C:93 , TRP C:96 , TYR C:112 , ILE C:116 , ARG C:119 , HIS C:120 , LYS C:125 , ASN C:126 , ILE C:137 , TYR C:141 , LEU C:142 , PHE C:145 , ILE C:146 , TRP C:185 , CYN C:201 , HOH C:2097 , HOH C:2098 , HOH C:2118 , HOH C:2124	BINDING SITE FOR RESIDUE HEM C 200
06	AC6	SOFTWARE	TRP C:60 , TYR C:61 , PHE C:93 , HEM C:200	BINDING SITE FOR RESIDUE CYN C 201
07	AC7	SOFTWARE	ARG A:122 , THR A:123 , GLN A:127 , GLY A:161 , HOH A:2103 , HOH A:2107 , HOH A:2131	BINDING SITE FOR RESIDUE GOL A1196
08	AC8	SOFTWARE	PRO C:164 , LYS C:191 , TYR C:192 , HOH C:2154 , HOH C:2159	BINDING SITE FOR RESIDUE GOL C1196
09	AC9	SOFTWARE	PRO A:77 , ASP A:78 , GLY A:79 , THR C:59 , THR C:152 , HOH C:2140	BINDING SITE FOR RESIDUE GOL C1197
10	BC1	SOFTWARE	ARG B:95 , LEU B:98 , ASN B:102 , HOH B:2117 , GLN C:43 , SER C:101 , ASN C:102 , ARG C:103 , SER C:104 , TYR C:105	BINDING SITE FOR RESIDUE EPE C1198
11	BC2	SOFTWARE	THR B:100 , SER B:101 , ASN B:102 , ARG B:103 , SER B:104 , TYR B:105 , HOH B:2069 , HOH B:2182 , ARG C:95 , LEU C:98 , ASN C:102	BINDING SITE FOR RESIDUE EPE B1196

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

(no "Cis Peptide Bond" information available for 3ZJM)

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

(no "PROSITE Motif" information available for 3ZJM)

(no "Exon" information available for 3ZJM)

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:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjm A   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPFTATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjm B   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPFTATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain C from PDB  Type:PROTEIN  Length:191
 aligned with Q8TLY9_METAC | Q8TLY9 from UniProtKB/TrEMBL  Length:195

    Alignment length:191
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194 
         Q8TLY9_METAC     5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTCNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPITATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zjm C   5 KIPGYTYGETENRAPFNLEDLKLLKEAVMFTAEDEEYIQKAGEVLEDQVEEILDTWYGFVGSHPHLLYYFTSPDGTPNEKYLAAVRKRFSRWILDTSNRSYDQAWLDYQYEIGLRHHRTKKNQTDNVESVPNIGYRYLVAFIYPFTATMKPFLARKGHTPEEVEKMYQAWFKATTLQVALWSYPYVKYGDF 195
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q8TLY9_METAC | Q8TLY9)


GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3zjm)

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3zjh	TRP(60)B9ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zji	TYR(61)B10ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjj	PHE(93)E11LEU MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjl	LEU(142)G4ALA MUTATION OF M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjn	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE
3zjo	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH AZIDE
3zjp	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH IMIDAZOLE
3zjq	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH NICOTINAMIDE
3zjr	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH CYANIDE AND XENON
3zjs	M.ACETIVORANS PROTOGLOBIN IN COMPLEX WITH AZIDE AND XENON

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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CATH Domains (0, 0)

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Gene Ontology (3, 3)

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