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Title :   CRYSTAL STRUCTURE OF A 3-HYDROXYPROLINE DEHYDRATSE FROM AGROBACTERIUM VITIS, TARGET EFI-506470, WITH BOUND PYRROLE 2-CARBOXYLATE, ORDERED ACTIVE SITE

Authors :   M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wa S. Sojitra, M. Stead, E. Washington, A. Scott Glenn, S. Chowdhury, B. J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerl S. C. Almo, Enzyme Function Initiative (Efi)

Date :   17 Apr 13 (Deposition) - 01 May 13 (Release) - 01 May 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : B,D

Keywords :   Proline Racemase Family, Proposed 3-Oh Proline Dehydratase, Enzyme Function Initiative, Efi, Structural Genomics, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, R. Toro, R. Bhosle, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitra, M. Stead, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, B. Hillerich, J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Function Initiative (Efi)
Crystal Structure Of A 3-Hydroxyproline Dehydratse From Agrobacterium Vitis, Target Efi-506470, With Bound Pyrrole 2-Carboxylate, Ordered Active Site
To Be Published
PubMed: search

Molecule 1 - 3-HYDROXYPROLINE DEHYDRATSE
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AVI_7022
	Organism Scientific	:	AGROBACTERIUM VITIS S4
	Organism Taxid	:	311402
	Strain	:	S4

		1	2
Asymmetric/Biological Unit	:	B	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CIT	2	Ligand/Ion	CITRIC ACID
3	PYC	2	Ligand/Ion	PYRROLE-2-CARBOXYLATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:152 , THR B:164 , ASP B:166 , ILE B:176 , VAL B:177 , ASP B:178 , THR B:228 , ARG B:270 , HOH B:1085 , HOH B:1151 , HOH B:1158 , HOH B:1159 , HOH B:1204	BINDING SITE FOR RESIDUE CIT B 901
2	AC2	SOFTWARE	ASP B:85 , PRO B:88 , ASP B:172 , SER B:173 , TRP B:219 , ASN B:220 , HIS B:221 , SER B:223 , HOH B:1317	BINDING SITE FOR RESIDUE ACT B 902
3	AC3	SOFTWARE	ALA D:152 , THR D:164 , ASP D:166 , ILE D:176 , VAL D:177 , ASP D:178 , THR D:228 , ARG D:270 , HOH D:596 , HOH D:622 , HOH D:665	BINDING SITE FOR RESIDUE CIT B 903
4	AC4	SOFTWARE	GLU B:17 , SER B:90 , GLY B:91 , SER B:92 , ASP B:252 , THR B:256 , GLY B:257 , THR B:258	BINDING SITE FOR RESIDUE PYC B 904
5	AC5	SOFTWARE	GLU D:17 , HIS D:62 , GLU D:82 , SER D:90 , GLY D:91 , SER D:92 , ASP D:252 , THR D:256 , GLY D:257 , THR D:258	BINDING SITE FOR RESIDUE PYC D 401

(no "SS Bond" information available for 4K7G)

Asymmetric/Biological Unit

No.	Residues
1	Glu B:54	-	Pro B:55
2	Glu B:111	-	Pro B:112
3	Arg B:247	-	Pro B:248
4	Glu D:54	-	Pro D:55
5	Glu D:111	-	Pro D:112
6	Arg D:247	-	Pro D:248

(no "SAP(SNP)/Variant" information available for 4K7G)

(no "PROSITE Motif" information available for 4K7G)

(no "Exon" information available for 4K7G)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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	SAPs(SNPs)	PROSITE motifs	Exons
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Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4k7gb_ B: automated matches                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................hhhhhhhhhhhhhhhhhhhhh....................................hhhhhhhhhhhhhhh..................................................................................hhhhhhhhhhhhhhhhhhhhhhh..............................................hhhhhhhhhhhhhhh........................................................................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k7g B   5 KVIHVIGVHAEGEVGDVIVGGVSPPPGDTLWEQSRFIASDETLRNFVLNEPRGGVFRHVNLLVPPKDPRAQMGFIIMEPADTPPMSGSNSICVSTAILDSGIISMQEPLTHMVLEAPGGVIEVTAECANGKAERINVLNVASFVTRLAAALEVEGLGTLTVDTAYGGDSFVIVDAIGLGFSLKPDEARELAELGMKITAAANEQLGFVHPCNADWNHISFCQMTTPITRENGILTGKSAVAIRPGKIDRSPTGTGCSARLAVMHARGEIGIGETYIGRSIIDSEFKCHIDSLTEIGGLSAIRPVISGRAWITGVSQLMLDPTDPWPSGYQLSDTWPAI 342
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334

Chain D from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4k7gd_ D: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..............................hhhhhhhhhhhhhhhhhhhhh....................................hhhhhhhhhhhhhhh..................................................................................hhhhhhhhhhhhhhhhhhhhhhh..............................................hhhhhhhhhhhhhhh........................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k7g D  -9 LGTENLYFQSMRTNKVIHVIGVHAEGEVGDVIVGGVSPPPGDTLWEQSRFIASDETLRNFVLNEPRGGVFRHVNLLVPPKDPRAQMGFIIMEPADTPPMSGSNSICVSTAILDSGIISMQEPLTHMVLEAPGGVIEVTAECANGKAERINVLNVASFVTRLAAALEVEGLGTLTVDTAYGGDSFVIVDAIGLGFSLKPDEARELAELGMKITAAANEQLGFVHPCNADWNHISFCQMTTPITRENGILTGKSAVAIRPGKIDRSPTGTGCSARLAVMHARGEIGIGETYIGRSIIDSEFKCHIDSLTEIGGLSAIRPVISGRAWITGVSQLMLDPTDPWPSGYQLSDTWPAI 342
                                     0        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       300       310       320       330       340

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Diaminopimelate epimerase-like (37)

Superfamily: Diaminopimelate epimerase-like (37)

Family: automated matches (15)

Protein domain: automated matches (15)

Agrobacterium vitis [TaxId: 311402] (2)

1a	d4k7gb_	B:
1b	d4k7gd_	D:

(no "CATH Domain" information available for 4K7G)

(no "Pfam Domain" information available for 4K7G)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PYC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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	Cis Peptide Bonds
		Arg B:247 - Pro B:248	[ RasMol ]
		Arg D:247 - Pro D:248	[ RasMol ]
		Glu B:111 - Pro B:112	[ RasMol ]
		Glu B:54 - Pro B:55	[ RasMol ]
		Glu D:111 - Pro D:112	[ RasMol ]
		Glu D:54 - Pro D:55	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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