2ZDO - JenaLib

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Title :   CRYSTAL STRUCTURE OF ISDG-N7A IN COMPLEX WITH HEMIN

Authors :   W. C. Lee, M. L. Reniere, E. P. Skaar, M. E. P. Murphy

Date :   27 Nov 07 (Deposition) - 19 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Ruffling, Protein-Substrate Complex, Cytoplasm, Heme, Iron, Metal-Binding, Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. C. Lee, M. L. Reniere, E. P. Skaar, M. E. P. Murphy
Ruffling Of Metalloporphyrins Bound To Isdg And Isdi, Two Heme-Degrading Enzymes In Staphylococcus Aureus
J. Biol. Chem. V. 283 30957 2008
PubMed-ID: 18713745 | Reference-DOI: 10.1074/JBC.M709486200
(for further references see the PDB file header)

Molecule 1 - HEME-DEGRADING MONOOXYGENASE ISDG
	Chains	:	A, B, C, D
	EC Number	:	1.14.99.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ISDG
	Mutation	:	YES
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS
	Organism Taxid	:	1280
	Strain	:	N315
	Synonym	:	IRON-REGULATED SURFACE DETERMINANT ISDG, IRON- RESPONSIVE SURFACE DETERMINANT ISDG, HEME OXYGENASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:5 , ALA A:7 , ARG A:22 , PHE A:23 , ARG A:26 , HIS A:27 , GLY A:28 , ILE A:29 , ILE A:54 , THR A:56 , TRP A:67 , ALA A:76 , HIS A:77 , ASN A:94 , HOH A:202 , HOH A:253 , HOH A:263	BINDING SITE FOR RESIDUE HEM A 200
2	AC2	SOFTWARE	ALA B:5 , ALA B:7 , ARG B:22 , PHE B:23 , ARG B:26 , HIS B:27 , GLY B:28 , ILE B:29 , ILE B:54 , THR B:56 , PHE B:64 , TRP B:67 , ALA B:76 , HIS B:77 , ASN B:94 , HOH B:215 , HOH B:282 , HOH B:283	BINDING SITE FOR RESIDUE HEM B 200
3	AC3	SOFTWARE	ALA C:5 , ALA C:7 , ARG C:22 , PHE C:23 , ARG C:26 , HIS C:27 , GLY C:28 , ILE C:29 , ILE C:54 , THR C:56 , TRP C:67 , ALA C:76 , HIS C:77 , ASN C:94 , HOH C:204 , HOH C:232	BINDING SITE FOR RESIDUE HEM C 200
4	AC4	SOFTWARE	ALA D:5 , ALA D:7 , ARG D:22 , PHE D:23 , ARG D:26 , HIS D:27 , GLY D:28 , ILE D:29 , ILE D:54 , THR D:56 , PHE D:64 , TRP D:67 , ALA D:76 , HIS D:77 , ILE D:91 , ASN D:94 , HOH D:202 , HOH D:241	BINDING SITE FOR RESIDUE HEM D 200

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

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABM	PS51725	ABM domain profile.	HDOX1_STAAN	3-92	4	A:3-92 B:3-92 C:3-92 D:3-92

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABM	PS51725	ABM domain profile.	HDOX1_STAAN	3-92	2	A:3-92 B:3-92 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABM	PS51725	ABM domain profile.	HDOX1_STAAN	3-92	2	- - C:3-92 D:3-92

(no "Exon" information available for 2ZDO)

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:108
 aligned with HDOX1_STAAN | Q7A649 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:108
                             1                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99        
          HDOX1_STAAN     - -MKFMAENRLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
               SCOP domains d2zdoa_ A: automated matches                                                                                 SCOP domains
               CATH domains 2zdoA00 A:0-107  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhh....hhhhh..eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---ABM  PDB: A:3-92 UniProt: 3-92                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zdo A   0 TMKFMAEARLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
                                     9        19        29        39        49        59        69        79        89        99

Chain B from PDB  Type:PROTEIN  Length:108
 aligned with HDOX1_STAAN | Q7A649 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:108
                             1                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99        
          HDOX1_STAAN     - -MKFMAENRLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
               SCOP domains d2zdob_ B: automated matches                                                                                 SCOP domains
               CATH domains 2zdoB00 B:0-107  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhh..hhhhh..eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---ABM  PDB: B:3-92 UniProt: 3-92                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zdo B   0 TMKFMAEARLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
                                     9        19        29        39        49        59        69        79        89        99

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with HDOX1_STAAN | Q7A649 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:108
                             1                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99        
          HDOX1_STAAN     - -MKFMAENRLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
               SCOP domains d2zdoc_ C: automated matches                                                                                 SCOP domains
               CATH domains 2zdoC00 C:0-107  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeee..hhhhhhhhhhh..hhhhh..eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---ABM  PDB: C:3-92 UniProt: 3-92                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zdo C   0 TMKFMAEARLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
                                     9        19        29        39        49        59        69        79        89        99

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with HDOX1_STAAN | Q7A649 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:109
                              1                                                                                                          
                              |      8        18        28        38        48        58        68        78        88        98         
          HDOX1_STAAN     - --MKFMAENRLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
               SCOP domains d2zdod_ D: automated matches                                                                                  SCOP domains
               CATH domains 2zdoD00 D:-1-107  [code=3.30.70.900, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhh..hhhhh..eeeeeeeee.....eeeeeeeeee.hhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ABM  PDB: D:3-92 UniProt: 3-92                                                            --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2zdo D  -1 STMKFMAEARLTLTKGTAKDIIERFYTRHGIETLEGFDGMFVTQTLEQEDFDEVKILTVWKSKQAFTDWLKSDVFKAAHKHVRSKNEDESSPIINNKVITYDIGYSYMK 107
                                     8        18        28        38        48        58        68        78        88        98

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: Dimeric alpha+beta barrel (122)

Family: PG130-like (12)

Protein domain: automated matches (1)

Staphylococcus aureus [TaxId: 1280] (1)

1a	d2zdoa_	A:
1b	d2zdob_	B:
1c	d2zdoc_	C:
1d	d2zdod_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.900, no name defined] (47)

Staphylococcus aureus. Organism_taxid: 1280. Strain: n315. (2)

1a	2zdoA00	A:0-107
1b	2zdoB00	B:0-107
1c	2zdoC00	C:0-107
1d	2zdoD00	D:-1-107

(no "Pfam Domain" information available for 2ZDO)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HDOX1_STAAN | Q7A649)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0004392	heme oxygenase (decyclizing) activity	Catalysis of the reaction: heme + 3 donor-H2 + 3 O2 = biliverdin + Fe2+ + CO + 3 acceptor + 3 H2O.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
	GO:0042167	heme catabolic process	The chemical reactions and pathways resulting in the breakdown of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0033212	iron assimilation	A process in which iron is solubilized and transported into a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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