3E0L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   COMPUTATIONALLY DESIGNED AMMELIDE DEAMINASE

Authors :   P. M. Murphy, J. M. Bolduc, J. L. Gallaher, B. L. Stoddard, D. Baker

Date :   31 Jul 08 (Deposition) - 03 Mar 09 (Release) - 01 Dec 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.37

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

Keywords :   Computational-Design Backbone-Flexibility Loop-Remodeling Guanine Cytosine Ammelide Deaminase, Hydrolase, Metal- Binding, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. M. Murphy, J. M. Bolduc, J. L. Gallaher, B. L. Stoddard, D. Baker
Alteration Of Enzyme Specificity By Computational Loop Remodeling And Design.
Proc. Natl. Acad. Sci. Usa V. 106 9215 2009
PubMed-ID: 19470646 | Reference-DOI: 10.1073/PNAS.0811070106
(for further references see the PDB file header)

Molecule 1 - GUANINE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.4.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	R5-5
	Expression System Strain	:	BL21(DE3)*
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET15B
	Gene	:	GDA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GUANASE, GUANINE AMINASE, GUANINE AMINOHYDROLASE, GAH, P51-NEDASIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:82 , HIS A:84 , HIS A:238 , ASP A:328 , HOH A:1463	BINDING SITE FOR RESIDUE ZN A 1452
2	AC2	SOFTWARE	HIS B:82 , HIS B:84 , HIS B:238 , ASP B:328 , HOH B:1468	BINDING SITE FOR RESIDUE ZN B 1452

(no "SS Bond" information available for 3E0L)

Asymmetric/Biological Unit

No.	Residues
1	Val A:329	-	Ala A:330
2	Val A:446	-	Pro A:447
3	Val B:329	-	Ala B:330
4	Val B:446	-	Pro B:447

(no "SAP(SNP)/Variant" information available for 3E0L)

(no "PROSITE Motif" information available for 3E0L)

Asymmetric/Biological Unit (14, 28)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000358399	1d	ENSE00001951441	chr9:74764383-74764598	216	GUAD_HUMAN	1-41	41	2	A:8-41 B:8-41	34 34
1.3a	ENST00000358399	3a	ENSE00001751942	chr9:74810416-74810504	89	GUAD_HUMAN	42-71	30	2	A:42-71 B:42-71	30 30
1.5	ENST00000358399	5	ENSE00001626863	chr9:74817487-74817658	172	GUAD_HUMAN	71-128	58	2	A:71-128 B:71-128	58 58
1.6a	ENST00000358399	6a	ENSE00001774554	chr9:74825603-74825690	88	GUAD_HUMAN	129-158	30	2	A:129-158 B:129-158	30 30
1.7	ENST00000358399	7	ENSE00001706302	chr9:74828802-74828907	106	GUAD_HUMAN	158-193	36	2	A:158-193 B:158-193	36 36
1.9	ENST00000358399	9	ENSE00001591719	chr9:74834395-74834422	28	GUAD_HUMAN	193-202	10	2	A:193-202 B:193-202	10 10
1.10	ENST00000358399	10	ENSE00001722211	chr9:74838036-74838143	108	GUAD_HUMAN	203-238	36	2	A:203-236 (gaps) B:203-236 (gaps)	36 36
1.11	ENST00000358399	11	ENSE00001672840	chr9:74840593-74840700	108	GUAD_HUMAN	239-274	36	2	A:237-272 B:237-272	36 36
1.12a	ENST00000358399	12a	ENSE00001749359	chr9:74842859-74842956	98	GUAD_HUMAN	275-307	33	2	A:273-305 B:273-305	33 33
1.13	ENST00000358399	13	ENSE00002175571	chr9:74846030-74846097	68	GUAD_HUMAN	307-330	24	2	A:305-328 B:305-328	24 24
1.14	ENST00000358399	14	ENSE00001760403	chr9:74856068-74856214	147	GUAD_HUMAN	330-379	50	2	A:328-377 B:328-377	50 50
1.15	ENST00000358399	15	ENSE00001767251	chr9:74860064-74860194	131	GUAD_HUMAN	379-422	44	2	A:377-420 B:377-420	44 44
1.16	ENST00000358399	16	ENSE00001624681	chr9:74862322-74862349	28	GUAD_HUMAN	423-432	10	2	A:421-430 B:421-430	10 10
1.17c	ENST00000358399	17c	ENSE00001646828	chr9:74863188-74867140	3953	GUAD_HUMAN	432-454	23	2	A:430-449 B:430-449	20 20

Asymmetric/Biological 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:442
 aligned with GUAD_HUMAN | Q9Y2T3 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:444
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
           GUAD_HUMAN     8 PLAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPFS 451
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee.......eeeeeeeeee.....eeeeee..hhhhhhhhh..hhh.eee.....eeee.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhhhhhhhhhhh.eeeee.ee............hhhhhhhhhhhhhhhhhh.....eeeeeee--....hhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhh....hhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeehhhhhhhh.....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh................eeee..................hhhhhhhhhhhhhh....eeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: A:8-41            Exon 1.3a  PDB: A:42-71       ---------------------------------------------------------Exon 1.6a  PDB: A:129-158     ----------------------------------Exon 1.9  Exon 1.10  PDB: A:203-236 (gaps)    Exon 1.11  PDB: A:237-272           Exon 1.12a  PDB: A:273-305       ----------------------Exon 1.14  PDB: A:328-377 UniProt: 330-379        -------------------------------------------Exon 1.16 ------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.5  PDB: A:71-128 UniProt: 71-128                   -----------------------------Exon 1.7  PDB: A:158-193            -----------------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:305-32------------------------------------------------Exon 1.15  PDB: A:377-420 UniProt: 379-422  ---------Exon 1.17c           Transcript 1 (2)
                 3e0l A   8 PLAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTP--GNGVSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPFS 449
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    |  215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445    
                                                                                                                                                                                                                                      212  |                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                         213

Chain B from PDB  Type:PROTEIN  Length:442
 aligned with GUAD_HUMAN | Q9Y2T3 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:444
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447    
           GUAD_HUMAN     8 PLAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTPRFSLSCSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPFS 451
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeeeeeeeee.....eeeeee..hhhhhhhhh..hhhhhee.....eeee.eeeeeee.hhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhh.eeeee.ee............hhhhhhhhhhhhhhhhhh.....eeeeeee--....hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh....hhhhhhhh.......eeeee....hhhhhhhhhhhh.eeeehhhhhhhh.....hhhhhhhh..eeee..........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh................eeee..................hhhhhhhhhhhhhhhhh.eeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1d  PDB: B:8-41            Exon 1.3a  PDB: B:42-71       ---------------------------------------------------------Exon 1.6a  PDB: B:129-158     ----------------------------------Exon 1.9  Exon 1.10  PDB: B:203-236 (gaps)    Exon 1.11  PDB: B:237-272           Exon 1.12a  PDB: B:273-305       ----------------------Exon 1.14  PDB: B:328-377 UniProt: 330-379        -------------------------------------------Exon 1.16 ------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.5  PDB: B:71-128 UniProt: 71-128                   -----------------------------Exon 1.7  PDB: B:158-193            -----------------------------------------------------------------------------------------------------------------Exon 1.13  PDB: B:305-32------------------------------------------------Exon 1.15  PDB: B:377-420 UniProt: 379-422  ---------Exon 1.17c           Transcript 1 (2)
                 3e0l B   8 PLAHIFRGTFVHSTWTCPMEVLRDHLLGVSDSGKIVFLEEASQQEKLAKEWCFKPCEIRELSHHEFFMPGLVDTHIHASQYSFAGSSIDLPLLEWLTKYTFPAEHRFQNIDFAEEVYTRVVRRTLKNGTTTACYFATIHTDSSLLLADITDKFGQRAFVGKVCMDLNDTFPEYKETTEESIKETERFVSEMLQKNYSRVKPIVTP--GNGVSETLMGELGNIAKTRDLHIQSHISENRDEVEAVKNLYPSYKNYTSVYDKNNLLTNKTVMAHGCYLSAEELNVFHERGASIAHCPNSNLSLSSGFLNVLEVLKHEVKIGLGTDVAGGYSYSMLDAIRRAVMVSNILLINKVNEKSLTLKEVFRLATLGGSQALGLDGEIGNFEVGKEFDAILINPKASDSPIDLFYGDFFGDISEAVIQKFLYLGDDRNIEEVYVGGKQVVPFS 449
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    |  215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445    
                                                                                                                                                                                                                                      212  |                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                         213

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 3E0L)

(no "CATH Domain" information available for 3E0L)

(no "Pfam Domain" information available for 3E0L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GUAD_HUMAN | Q9Y2T3)

molecular function
	GO:0008892	guanine deaminase activity	Catalysis of the reaction: guanine + H2O = xanthine + NH3.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006147	guanine catabolic process	The chemical reactions and pathways resulting in the breakdown of guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
	GO:0046098	guanine metabolic process	The chemical reactions and pathways involving guanine, 2-amino-6-hydroxypurine, a purine that is one of the five main bases found in nucleic acids and a component of a number of phosphorylated guanosine derivatives whose metabolic or regulatory functions are important.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:0006139	nucleobase-containing compound metabolic process	Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
	GO:0006195	purine nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Val A:329 - Ala A:330	[ RasMol ]
		Val A:446 - Pro A:447	[ RasMol ]
		Val B:329 - Ala B:330	[ RasMol ]
		Val B:446 - Pro B:447	[ RasMol ]

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	3e0l
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Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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Exons (14, 28)

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