2VGR - JenaLib

Title :   STRUCTURE OF THE WT-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 :   15 Nov 07 (Deposition) - 05 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Compounds

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

Structural Features

Chains, Units

		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)

Ligands, Modified Residues, Ions (1, 4)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	BLA	4	Ligand/Ion	BILIVERDINE IX ALPHA

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	BLA	1	Ligand/Ion	BILIVERDINE IX ALPHA

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:79 , ASN A:88 , ASP A:105 , MET A:107 , PHE A:109 , ILE A:115 , TYR A:141 , PHE A:143 , PHE A:144 , TYR A:158 , MET A:202 , ASP A:206 , PRO A:207 , VAL A:208 , TYR A:211	BINDING SITE FOR RESIDUE BLA A1234
2	AC2	SOFTWARE	ILE B:79 , ILE B:86 , ASN B:88 , GLY B:103 , MET B:104 , ASP B:105 , MET B:107 , PHE B:109 , VAL B:117 , GLN B:121 , ARG B:142 , PHE B:143 , TYR B:158 , MET B:202 , ASP B:206 , VAL B:208 , TYR B:211	BINDING SITE FOR RESIDUE BLA B1234
3	AC3	SOFTWARE	ILE C:79 , ASN C:88 , ASP C:105 , MET C:107 , PHE C:109 , ILE C:115 , TYR C:141 , PHE C:143 , PHE C:144 , TYR C:158 , MET C:202 , LEU C:205 , ASP C:206 , PRO C:207 , VAL C:208 , TYR C:211 , PHE C:230	BINDING SITE FOR RESIDUE BLA C1234
4	AC4	SOFTWARE	ILE D:79 , ASN D:88 , ILE D:90 , GLY D:103 , MET D:104 , ASP D:105 , MET D:107 , PHE D:109 , VAL D:117 , GLN D:121 , ARG D:142 , PHE D:143 , TYR D:158 , MET D:202 , PRO D:207 , TYR D:211 , HOH D:2077	BINDING SITE FOR RESIDUE BLA D1234

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Asymmetric Unit

No.	Residues
1	Glu A:136	-	Asp A:137
2	Asp A:137	-	Asp A:138
3	Asp A:138	-	Gly A:139
4	Asp A:206	-	Pro A:207
5	Tyr B:141	-	Arg B:142
6	Gly C:56	-	Gly C:57
7	Asp C:111	-	Lys C:112
8	Asp C:206	-	Pro C:207

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:210
 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....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vgr A  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNV---GGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50 |   |  60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
                                                          52  56

Chain B from PDB  Type:PROTEIN  Length:211
 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.................................eeeee...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vgr B  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTK--GDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50   |  | 60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
                                                            54 57

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with PEBS_BPPRM | Q58MU6 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:215
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228     
           PEBS_BPPRM    19 KSKTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh...eeeeeeeeeeeeee.--.eeeeeeeeeeee..eeeeeeeeeee..eeeeeeeeee.......eeeeeeee.....eeeeeeee.................................eeeee...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vgr C  19 KSKTIWQNYIDALFETFPQLEISEVWAKWDGGNVT--GGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
                                    28        38        48    |  |58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228     
                                                             53 56

Chain D from PDB  Type:PROTEIN  Length:213
 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-2vgrD01 D:25-231                                                                                                                                                                                  -- Pfam domains (1)
           Pfam domains (2) ----Fe_bilin_red-2vgrD02 D:25-231                                                                                                                                                                                  -- Pfam domains (2)
           Pfam domains (3) ----Fe_bilin_red-2vgrD03 D:25-231                                                                                                                                                                                  -- Pfam domains (3)
           Pfam domains (4) ----Fe_bilin_red-2vgrD04 D:25-231                                                                                                                                                                                  -- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeeeeee....eeeeeeeeeee...eeeeeeeeeee..eeeeeeeeee.......eeeeeeee.....eeeeeeee.................................eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vgr D  21 KTIWQNYIDALFETFPQLEISEVWAKWDGGNVTKDGGDAKLTANIRTGEHFLKAREAHIVDPNSDIYNTILYPKTGADLPCFGMDLMKFSDKKVIIVFDFQHPREKYLFSVDGLPEDDGKYRFFEMGNHFSKNIFVRYCKPDEVDQYLDTFKLYLTKYKEMIDNNKPVGEDTTVYSDFDTYMTELDPVRGYMKNKFGEGRSEAFVNDFLFSYK 233
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Legend:		→ Mismatch	(orange background)
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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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (5, 5)

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	Cis Peptide Bonds
		Asp A:137 - Asp A:138	[ RasMol ]
		Asp A:138 - Gly A:139	[ RasMol ]
		Asp A:206 - Pro A:207	[ RasMol ]
		Asp C:111 - Lys C:112	[ RasMol ]
		Asp C:206 - Pro C:207	[ RasMol ]
		Glu A:136 - Asp A:137	[ RasMol ]
		Gly C:56 - Gly C:57	[ RasMol ]
		Tyr B:141 - Arg B:142	[ RasMol ]

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Related Entries

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Related Entries Specified in the PDB File

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

Description