2VCK - JenaLib

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Title :   STRUCTURE OF PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA

Authors :   T. Dammeyer, E. Hofmann, N. Frankenberg-Dinkel

Date :   25 Sep 07 (Deposition) - 05 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  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Cyanophages, Biliverdin Ixa, Oxidoreductase, Phycobilin Reductase, Phycobilin Synthesis, Prochlorococcus, Phycoerythrobilin, Biliverdin Reductase, Ferredoxin Dependent (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Dammeyer, E. Hofmann, N. Frankenberg-Dinkel
Phycoerythrobilin Synthase (Pebs) Of A Marine Virus: Crystal Structures Of The Biliverdin Complex And The Substrate-Free Form.
J. Biol. Chem. V. 283 27547 2008
PubMed-ID: 18662988 | Reference-DOI: 10.1074/JBC.M803765200

Molecule 1 - CYANOBACTERIAL PHYCOERYTHROBILIN
	Chains	:	A, B, C, D
	EC Number	:	1.3.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	PROCHLOROCOCCUS PHAGE P-SSM2
	Organism Taxid	:	268746
	Synonym	:	PHYCOBILIN REDUCTASE, CYANOPHAGE PHYCOERYTHROBILIN SYNTHASE PEBS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 28)

No.	Name	Count	Type	Full Name
1	BLA	4	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (2, 7)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (2, 7)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:79 , ILE A:86 , ASN A:88 , ILE A:90 , GLY A:103 , ASP A:105 , MSE A:107 , PHE A:109 , ILE A:115 , VAL A:117 , GLN A:121 , TYR A:141 , ARG A:142 , PHE A:143 , PHE A:144 , TYR A:158 , MSE A:202 , ASP A:206 , VAL A:208 , TYR A:211 , HOH A:2108 , HOH A:2125	BINDING SITE FOR RESIDUE BLA A1234
2	AC2	SOFTWARE	ARG A:142 , ILE B:79 , ILE B:86 , ASN B:88 , ILE B:90 , ASP B:105 , MSE B:107 , LYS B:113 , ILE B:115 , VAL B:117 , GLN B:121 , TYR B:141 , ARG B:142 , PHE B:143 , PHE B:144 , PHE B:150 , TYR B:158 , MSE B:202 , ASP B:206 , PRO B:207 , VAL B:208 , TYR B:211 , HOH B:2126	BINDING SITE FOR RESIDUE BLA B1234
3	AC3	SOFTWARE	ILE C:79 , ILE C:86 , ASN C:88 , ILE C:90 , ASP C:105 , MSE C:107 , ILE C:115 , VAL C:117 , GLN C:121 , TYR C:141 , ARG C:142 , PHE C:143 , PHE C:144 , TYR C:158 , MSE C:202 , ASP C:206 , VAL C:208 , TYR C:211 , HOH C:2130	BINDING SITE FOR RESIDUE BLA C1234
4	AC4	SOFTWARE	ASN D:88 , ILE D:90 , GLY D:103 , MSE D:104 , ASP D:105 , MSE D:107 , GLN D:121 , ARG D:142 , PHE D:143 , PHE D:144 , TYR D:158 , MSE D:202 , ASP D:206 , PRO D:207 , TYR D:211 , HOH D:2167	BINDING SITE FOR RESIDUE BLA D1234

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

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

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

(no "PROSITE Motif" information available for 2VCK)

(no "Exon" information available for 2VCK)

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:208
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:213
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           PEBS_BPPRM    21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeee...----..eeeeeeeeee..eeeeeeeeee....eeeeeeeee.......eeeeeeeeee..eeeeeeeee................-................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vck A  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNV----GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGmDLmKFSDKKVIIVFDFQHPREKYLFSVDGLPED-GKYRFFEmGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEmIDNNKPVGEDTTVYSDFDTYmTELDPVRGYmKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50 |    | 60        70        80        90       100   |  |110       120       130      |140     | 150       160       170       180|      190       200 |     210 |     220       230   
                                                          52   57                                            104-MSE                          137 |      |                                181-MSE              202-MSE   212-MSE                 
                                                                                                                107-MSE                         139      |                                                                                       
                                                                                                                                                       146-MSE

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:213
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           PEBS_BPPRM    21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeee...----..eeeeeeeeee..eeeeeeeeee....eeeeeeeee.......eeeeeeee.....eeeeeeee.................................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vck B  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNV----GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGmDLmKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEmGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEmIDNNKPVGEDTTVYSDFDTYmTELDPVRGYmKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50 |    | 60        70        80        90       100   |  |110       120       130       140     | 150       160       170       180|      190       200 |     210 |     220       230   
                                                          52   57                                            104-MSE                                   146-MSE                            181-MSE              202-MSE   212-MSE                 
                                                                                                                107-MSE

Chain C from PDB  Type:PROTEIN  Length:209
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:213
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           PEBS_BPPRM    21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeee...----..eeeeeeeeee..eeeeeeeeee....eeeeeeeee.......eeeeeeee.....eeeeeeee.................................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vck C  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNV----GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGmDLmKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEmGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEmIDNNKPVGEDTTVYSDFDTYmTELDPVRGYmKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50 |    | 60        70        80        90       100   |  |110       120       130       140     | 150       160       170       180|      190       200 |     210 |     220       230   
                                                          52   57                                            104-MSE                                   146-MSE                            181-MSE              202-MSE   212-MSE                 
                                                                                                                107-MSE

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:213
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
           PEBS_BPPRM    21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Fe_bilin_red-2vckD01 D:25-23    1                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) ----Fe_bilin_red-2vckD02 D:25-23    1                                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) ----Fe_bilin_red-2vckD03 D:25-23    1                                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) ----Fe_bilin_red-2vckD04 D:25-23    1                                                                                                                                                                              -- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeee...----..eeeeeeeeee..eeeeeeeeee....eeeeeeeee.......eeeeeeee.....eeeeeeee.................................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vck D  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNV----GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGmDLmKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEmGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEmIDNNKPVGEDTTVYSDFDTYmTELDPVRGYmKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50 |    | 60        70        80        90       100   |  |110       120       130       140     | 150       160       170       180|      190       200 |     210 |     220       230   
                                                          52   57                                            104-MSE                                   146-MSE                            181-MSE              202-MSE   212-MSE                 
                                                                                                                107-MSE

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 2VCK)

(no "CATH Domain" information available for 2VCK)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Fe_bilin_red] (8)

Family: Fe_bilin_red (8)

Prochlorococcus phage P-SSM2 (5)

1a	Fe_bilin_red-2vckD01	D:25-231
1b	Fe_bilin_red-2vckD02	D:25-231
1c	Fe_bilin_red-2vckD03	D:25-231
1d	Fe_bilin_red-2vckD04	D:25-231

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PEBS_BPPRM | Q58MU6)

molecular function
	GO:0050897	cobalt ion binding	Interacting selectively and non-covalently with a cobalt (Co) ion.
	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:0016636	oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces an iron-sulfur protein.
biological process
	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.
	GO:0010024	phytochromobilin biosynthetic process	The chemical reactions and pathways resulting in the formation of phytochromobilin, which involves the oxidative cleavage of heme by a heme oxygenase(HO) to form biliverdin IX alpha.

Asymmetric Unit
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	2vck
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	PEBS_BPPRM \| Q58MU6	:	2vcl 2vgr 2x9i 2x9j

2vcl	STRUCTURE OF THE PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN THE SUBSTRATE FREE FORM
2vgr	STRUCTURE OF THE WT-PHYCOERYTHROBILIN SYNTHASE PEBS FROM THE CYANOPHAGE P-SSM2 IN COMPLEX WITH THE BOUND SUBSTRATE BILIVERDIN IXA

Description

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Ligands, Modified Residues, Ions (2, 28)

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