1QY9 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF E. COLI SE-MET PROTEIN YDDE

Authors :   A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Camb Y. Bourne

Date :   10 Sep 03 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Putative Phenazine Biosynthesis Protein; Epimerase; Antibiotic Biosynthesis Protein; Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Grassick, G. Sulzenbacher, V. Roig-Zamboni, V. Campanacci, C. Cambillau, Y. Bourne
Crystal Structure Of E. Coli Ydde Protein Reveals A Strikin Homology With Diaminopimelate Epimerase
Proteins V. 55 764 2004
PubMed-ID: 15103639 | Reference-DOI: 10.1002/PROT.20025

Molecule 1 - HYPOTHETICAL PROTEIN YDDE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST17
	Expression System Strain	:	TUNER(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YDDE
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ORFB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 25)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	21	Mod. Amino Acid	SELENOMETHIONINE
3	OH	1	Ligand/Ion	HYDROXIDE ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	OH	-1	Ligand/Ion	HYDROXIDE ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	11	Mod. Amino Acid	SELENOMETHIONINE
3	OH	-1	Ligand/Ion	HYDROXIDE ION

Biological Unit 3 (2, 24)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	21	Mod. Amino Acid	SELENOMETHIONINE
3	OH	-1	Ligand/Ion	HYDROXIDE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS B:72 , GLY B:73	BINDING SITE FOR RESIDUE OH B 9072
2	AC2	SOFTWARE	CYS A:72 , GLY A:73 , HIS A:161 , LYS A:163 , THR A:225 , GLY A:226 , ASN A:227	BINDING SITE FOR RESIDUE GOL A 1000
3	AC3	SOFTWARE	CYS D:72 , GLY D:73 , HIS D:161 , LYS D:163 , THR D:225 , GLY D:226 , ASN D:227	BINDING SITE FOR RESIDUE GOL D 2000
4	AC4	SOFTWARE	ALA A:100 , GLY A:101 , LYS A:102 , HOH A:3056 , GLU D:32 , GLN D:36 , HOH D:2038	BINDING SITE FOR RESIDUE GOL A 3000

(no "SS Bond" information available for 1QY9)

Asymmetric Unit

No.	Residues
1	Phe A:25	-	Pro A:26
2	Phe B:25	-	Pro B:26
3	Phe C:25	-	Pro C:26
4	Phe D:25	-	Pro D:26

(no "SAP(SNP)/Variant" information available for 1QY9)

(no "PROSITE Motif" information available for 1QY9)

(no "Exon" information available for 1QY9)

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:295
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           YDDE_ECOLI     3 PQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains d1qy9a1 A:3-129 Hypothetical protein YddE                                                                                      d1qy9a2 A:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains 1qy9A01 A:3-121,A:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                 1qy9A02 A:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qy9A01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........eeeeeee.....hhhhhhhhhhhhh...eeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee....ee....hhhhhhhhhhhh..hhhhh......eeee....eeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.hhhh..eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qy9 A   3 PQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQmQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVmIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRmFSPAIGIVEDPVTGNANGPmGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGmIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                                    12        22        32  |     42        52        62        72        82        92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232       242       252       262 |     272       282       292     
                                                           35-MSE                                                                                                                           165-MSE                                        212-MSE             232-MSE                         264-MSE

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:295
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     
           YDDE_ECOLI     3 PQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains d1qy9b1 B:3-129 Hypothetical protein YddE                                                                                      d1qy9b2 B:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains 1qy9B01 B:3-121,B:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                 1qy9B02 B:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qy9B01       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........eeeeeee.....hhhhhhhhhhhhh...eeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee....ee....hhhhhhhhhhhh..hhhhh......eeee....eeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.......eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qy9 B   3 PQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQmQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVmIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRmFSPAIGIVEDPVTGNANGPmGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGmIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                                    12        22        32  |     42        52        62        72        82        92       102       112       122       132       142       152       162  |    172       182       192       202       212       222       232       242       252       262 |     272       282       292     
                                                           35-MSE                                                                                                                           165-MSE                                        212-MSE             232-MSE                         264-MSE

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:296
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291      
           YDDE_ECOLI     2 KPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains d1qy9c1 C:2-129 Hypothetical protein YddE                                                                                       d1qy9c2 C:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains 1qy9C01 C:2-121,C:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                  1qy9C02 C:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qy9C01       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........eeeeeee.....hhhhhhhhhhhhh..eeeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee....ee....hhhhhhhhhhhh..hhhhh......eeee....eeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.hhhh..eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qy9 C   2 KPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQmQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVmIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRmFSPAIGIVEDPVTGNANGPmGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGmIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                                    11        21        31   |    41        51        61        71        81        91       101       111       121       131       141       151       161   |   171       181       191       201       211|      221       231|      241       251       261  |    271       281       291      
                                                            35-MSE                                                                                                                           165-MSE                                        212-MSE             232-MSE                         264-MSE

Chain D from PDB  Type:PROTEIN  Length:297
 aligned with YDDE_ECOLI | P37757 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       
           YDDE_ECOLI     1 MKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
               SCOP domains d1qy9d1 D:1-129 Hypothetical protein YddE                                                                                        d1qy9d2 D:130-297 Hypothetical protein YddE                                                                                                                              SCOP domains
               CATH domains -1qy9D01 D:2-121,D:285-297 Diaminopimelate Epimerase; Chain A, domain 1                                                  1qy9D02 D:122-284 Diaminopimelate Epimerase; Chain A, domain 1                                                                                                     1qy9D01       CATH domains
           Pfam domains (1) -------PhzC-PhzF-1qy9D01 D:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (1)
           Pfam domains (2) -------PhzC-PhzF-1qy9D02 D:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (2)
           Pfam domains (3) -------PhzC-PhzF-1qy9D03 D:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (3)
           Pfam domains (4) -------PhzC-PhzF-1qy9D04 D:8-291                                                                                                                                                                                                                                                                   ------ Pfam domains (4)
         Sec.struct. author ...eeeeeee........eeeeeee.....hhhhhhhhhhhhh..eeeeee......eeeeee....ee..hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee..eeeeeee....ee....hhhhhhhhhhhh..hhhhh......eeee....eeeee.....hhhhh..hhhhhhhhhhhhh...eeeeee.....eeee.eeehhhheeee..hhhhhhhhhhhhhhh........eeeeeeee.hhhh..eeeeeeeeee..eeeeeeeee.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qy9 D   1 mKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQmQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVmIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRmFSPAIGIVEDPVTGNANGPmGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGmIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL 297
                            |       10        20        30    |   40        50        60        70        80        90       100       110       120       130       140       150       160    |  170       180       190       200       210 |     220       230 |     240       250       260   |   270       280       290       
                            1-MSE                            35-MSE                                                                                                                           165-MSE                                        212-MSE             232-MSE                         264-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Diaminopimelate epimerase-like (37)

Superfamily: Diaminopimelate epimerase-like (37)

Family: PhzC/PhzF-like (11)

Protein domain: Hypothetical protein YddE (3)

Escherichia coli [TaxId: 562] (3)

1a	d1qy9a1	A:3-129
1b	d1qy9a2	A:130-297
1c	d1qy9b1	B:3-129
1d	d1qy9b2	B:130-297
1e	d1qy9c1	C:2-129
1f	d1qy9c2	C:130-297
1g	d1qy9d1	D:1-129
1h	d1qy9d2	D:130-297

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Diaminopimelate Epimerase; Chain A, domain 1 (22)

Homologous Superfamily: Diaminopimelate Epimerase; Chain A, domain 1 (22)

Escherichia coli. Organism_taxid: 562. (3)

1a	1qy9C01	C:2-121,C:285-297
1b	1qy9D02	D:122-284
1c	1qy9D01	D:2-121,D:285-297
1d	1qy9A01	A:3-121,A:285-297
1e	1qy9B01	B:3-121,B:285-297
1f	1qy9A02	A:122-284
1g	1qy9B02	B:122-284
1h	1qy9C02	C:122-284

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DAP_epimerase (14)

Family: PhzC-PhzF (10)

Escherichia coli (strain K12) (3)

1a	PhzC-PhzF-1qy9D01	D:8-291
1b	PhzC-PhzF-1qy9D02	D:8-291
1c	PhzC-PhzF-1qy9D03	D:8-291
1d	PhzC-PhzF-1qy9D04	D:8-291

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (YDDE_ECOLI | P37757)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

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	Cis Peptide Bonds
		Phe A:25 - Pro A:26	[ RasMol ]
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		Phe C:25 - Pro C:26	[ RasMol ]
		Phe D:25 - Pro D:26	[ RasMol ]

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Access by PDB/NDB ID
	1qy9
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	YDDE_ECOLI \| P37757
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	YDDE_ECOLI \| P37757
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	YDDE_ECOLI \| P37757	:	1qya 1sdj

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 25)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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