3NIQ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA GUANIDINOPROPIONASE

Authors :   S. J. Lee, H. S. Kim, D. J. Kim, H. J. Yoon, K. H. Kim, J. Y. Yoon, J. Y. Jang, H S. W. Suh

Date :   16 Jun 10 (Deposition) - 01 Jun 11 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.07

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

Keywords :   Guanidinopropionase, Gpua, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Lee, D. J. Kim, H. S. Kim, B. I. Lee, H. J. Yoon, J. Y. Yoon, K. H. Kim, J. Y. Jang, H. N. Im, D. R. An, J. S. Song, H. J. Kim, S. W. Suh
Crystal Structures Of Pseudomonas Aeruginosa Guanidinobutyrase And Guanidinopropionase, Members Of The Ureohydrolase Superfamily
J. Struct. Biol. V. 175 329 2011
PubMed-ID: 21600989 | Reference-DOI: 10.1016/J.JSB.2011.05.002

Molecule 1 - 3-GUANIDINOPROPIONASE
	Chains	:	A, B
	EC Number	:	3.5.3.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21A(+)
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GPUA, PA0288
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PAO1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:16 , PHE A:17 , ASN A:50 , ARG A:51 , ASN A:63 , SER A:66 , LEU A:67 , HIS B:56 , ARG B:59	BINDING SITE FOR RESIDUE GOL A 1205
2	AC2	SOFTWARE	HIS A:126 , ASP A:148 , ASP A:152 , ASP A:240 , HOH A:367 , MN A:1602	BINDING SITE FOR RESIDUE MN A 1601
3	AC3	SOFTWARE	ASP A:148 , HIS A:150 , ASP A:240 , ASP A:242 , HOH A:367 , MN A:1601	BINDING SITE FOR RESIDUE MN A 1602
4	AC4	SOFTWARE	HIS B:126 , ASP B:148 , ASP B:152 , ASP B:240 , HOH B:371 , MN B:1604	BINDING SITE FOR RESIDUE MN B 1603
5	AC5	SOFTWARE	ASP B:148 , HIS B:150 , ASP B:240 , ASP B:242 , HOH B:371 , MN B:1603	BINDING SITE FOR RESIDUE MN B 1604

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

Asymmetric Unit

No.	Residues
1	Gly A:123	-	Gly A:124
2	Gly B:123	-	Gly B:124

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARGINASE_2	PS51409	Arginase family profile.	GPUA_PSEAE	25-311	2	A:25-311 B:25-311
2	ARGINASE_1	PS01053	Arginase family signature.	GPUA_PSEAE	238-259	2	A:238-259 B:238-259

Biological Unit 1 (2, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ARGINASE_2	PS51409	Arginase family profile.	GPUA_PSEAE	25-311	6	A:25-311 B:25-311
2	ARGINASE_1	PS01053	Arginase family signature.	GPUA_PSEAE	238-259	6	A:238-259 B:238-259

(no "Exon" information available for 3NIQ)

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:315
 aligned with GPUA_PSEAE | Q9I6K2 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
           GPUA_PSEAE     4 DHPQPLDAAEIPRFAGIPTFMRLPAFTDPAALQVGLIGVPWDGGTTNRAGARHGPREVRNLSSLMRKVHHVSRIAPYDLVRVGDLGDAPVNPIDLLDSLRRIEGFYRQVHAAGTLPLSVGGDHLVTLPIFRALGRERPLGMVHFDAHSDTNDRYFGDNPYTHGTPFRRAIEEGLLDPLRTVQIGIRGSVYSPDDDAFARECGIRVIHMEEFVELGVEATLAEARRVVGAGPTYVSFDVDVLDPAFAPGTGTPEIGGMTSLQAQQLVRGLRGLDLVGADVVEVSPPFDVGGATALVGATMMFELLCLLAESAARSA 318
               SCOP domains d3niqa_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh....hhhhh.eeeeee..........hhhhhhhhhhhhhhhh.........hhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh....eeeeee...................hhhhhhhhh..eeeeeeeeeee.........hhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh...eeeeee.hhh................hhhhhhhhhhh.....eeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------ARGINASE_2  PDB: A:25-311 UniProt: 25-311                                                                                                                                                                                                                                                      ------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ARGINASE_1            ----------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3niq A   4 DHPQPLDAAEIPRFAGIPTFMRLPAFTDPAALQVGLIGVPWDGGTTNRAGARHGPREVRNLSSLMRKVHHVSRIAPYDLVRVGDLGDAPVNPIDLLDSLRRIEGFYRQVHAAGTLPLSVGGDHLVTLPIFRALGRERPLGMVHFDAHSDTNDRYFGDNPYTHGTPFRRAIEEGLLDPLRTVQIGIRGSVYSPDDDAFARECGIRVIHMEEFVELGVEATLAEARRVVGAGPTYVSFDVDVLDPAFAPGTGTPEIGGMTSLQAQQLVRGLRGLDLVGADVVEVSPPFDVGGATALVGATMMFELLCLLAESAARSA 318
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with GPUA_PSEAE | Q9I6K2 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:313
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313   
           GPUA_PSEAE     4 DHPQPLDAAEIPRFAGIPTFMRLPAFTDPAALQVGLIGVPWDGGTTNRAGARHGPREVRNLSSLMRKVHHVSRIAPYDLVRVGDLGDAPVNPIDLLDSLRRIEGFYRQVHAAGTLPLSVGGDHLVTLPIFRALGRERPLGMVHFDAHSDTNDRYFGDNPYTHGTPFRRAIEEGLLDPLRTVQIGIRGSVYSPDDDAFARECGIRVIHMEEFVELGVEATLAEARRVVGAGPTYVSFDVDVLDPAFAPGTGTPEIGGMTSLQAQQLVRGLRGLDLVGADVVEVSPPFDVGGATALVGATMMFELLCLLAESAAR 316
               SCOP domains d3niqb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhh....hhhhh.eeeeee..........hhhhhhhhhhhhhhhh.........hhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh....eeeeee...................hhhhhhhhh..eeeeeeeeeee.........hhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhh................hhhhhhhhhhh....eeeeeeee..hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------ARGINASE_2  PDB: B:25-311 UniProt: 25-311                                                                                                                                                                                                                                                      ----- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ARGINASE_1            --------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3niq B   4 DHPQPLDAAEIPRFAGIPTFMRLPAFTDPAALQVGLIGVPWDGGTTNRAGARHGPREVRNLSSLMRKVHHVSRIAPYDLVRVGDLGDAPVNPIDLLDSLRRIEGFYRQVHAAGTLPLSVGGDHLVTLPIFRALGRERPLGMVHFDAHSDTNDRYFGDNPYTHGTPFRRAIEEGLLDPLRTVQIGIRGSVYSPDDDAFARECGIRVIHMEEFVELGVEATLAEARRVVGAGPTYVSFDVDVLDPAFAPGTGTPEIGGMTSLQAQQLVRGLRGLDLVGADVVEVSPPFDVGGATALVGATMMFELLCLLAESAAR 316
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313

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) (23833)

Fold: Arginase/deacetylase (138)

Superfamily: Arginase/deacetylase (138)

Family: automated matches (13)

Protein domain: automated matches (13)

Pseudomonas aeruginosa [TaxId: 208964] (3)

1a	d3niqa_	A:
1b	d3niqb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (GPUA_PSEAE | Q9I6K2)


GO:0047972	guanidinopropionase activity	Catalysis of the reaction: 3-guanidinopropanoate + H(2)O = beta-alanine + urea.
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:0016813	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines	Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amidine, a compound of the form R-C(=NH)-NH2.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:123 - Gly A:124	[ RasMol ]
		Gly B:123 - Gly B:124	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3niq
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GPUA_PSEAE \| Q9I6K2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.5.3.17
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	GPUA_PSEAE \| Q9I6K2
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	GPUA_PSEAE \| Q9I6K2	:	3nip

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File