3LA4 - 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 THE FIRST PLANT UREASE FROM JACK BEAN (CANAVALIA ENSIFORMIS)

Authors :   K. Ponnuraj

Date :   06 Jan 10 (Deposition) - 28 Jul 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Plant Urease, Jack Bean, Canavalia Ensiformis, Hydrolase, Metal- Binding, Nickel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Balasubramanian, K. Ponnuraj
Crystal Structure Of The First Plant Urease From Jack Bean: 83 Years Of Journey From Its First Crystal To Molecular Structure
J. Mol. Biol. V. 400 274 2010
PubMed-ID: 20471401 | Reference-DOI: 10.1016/J.JMB.2010.05.009

Molecule 1 - UREASE
	Chains	:	A
	EC Number	:	3.5.1.5
	Organism Common	:	HORSE BEAN
	Organism Scientific	:	CANAVALIA ENSIFORMIS
	Organism Taxid	:	3823
	Synonym	:	UREA AMIDOHYDROLASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (6x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	ACN	1	Ligand/Ion	ACETONE
2	CME	3	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NI	2	Ligand/Ion	NICKEL (II) ION
5	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (4, 42)

No.	Name	Count	Type	Full Name
1	ACN	6	Ligand/Ion	ACETONE
2	CME	18	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
3	KCX	6	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	NI	-1	Ligand/Ion	NICKEL (II) ION
5	PO4	12	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:407 , HIS A:409 , KCX A:490 , ASP A:633 , NI A:842 , PO4 A:843	BINDING SITE FOR RESIDUE NI A 841
2	AC2	SOFTWARE	KCX A:490 , HIS A:492 , HIS A:519 , HIS A:545 , GLY A:550 , NI A:841 , PO4 A:843	BINDING SITE FOR RESIDUE NI A 842
3	AC3	SOFTWARE	HIS A:407 , HIS A:409 , ALA A:440 , KCX A:490 , HIS A:492 , HIS A:519 , HIS A:545 , GLY A:550 , ASP A:633 , ALA A:636 , NI A:841 , NI A:842 , PO4 A:844	BINDING SITE FOR RESIDUE PO4 A 843
4	AC4	SOFTWARE	HIS A:492 , GLU A:493 , ASP A:494 , HIS A:519 , HIS A:593 , ARG A:609 , PO4 A:843	BINDING SITE FOR RESIDUE PO4 A 844
5	AC5	SOFTWARE	ARG A:222	BINDING SITE FOR RESIDUE ACN A 845

(no "SS Bond" information available for 3LA4)

Asymmetric Unit

No.	Residues
1	Ala A:554	-	Pro A:555
2	Arg A:575	-	Pro A:576
3	Glu A:742	-	Pro A:743

(no "SAP(SNP)/Variant" information available for 3LA4)

Asymmetric Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	UREA_CANEN	400-413	1	A:400-413
2	UREASE_3	PS51368	Urease domain profile.	UREA_CANEN	402-840	1	A:402-840
3	UREASE_2	PS00145	Urease active site.	UREA_CANEN	590-606	1	A:590-606

Biological Unit 1 (3, 18)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	UREASE_1	PS01120	Urease nickel ligands signature.	UREA_CANEN	400-413	6	A:400-413
2	UREASE_3	PS51368	Urease domain profile.	UREA_CANEN	402-840	6	A:402-840
3	UREASE_2	PS00145	Urease active site.	UREA_CANEN	590-606	6	A:590-606

(no "Exon" information available for 3LA4)

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:837
 aligned with UREA_CANEN | P07374 from UniProtKB/Swiss-Prot  Length:840

    Alignment length:840
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840
           UREA_CANEN     1 MKLSPREVEKLGLHNAGYLAQKRLARGVRLNYTEAVALIASQIMEYARDGEKTVAQLMCLGQHLLGRRQVLPAVPHLLNAVQVEATFPDGTKLVTVHDPISRENGELQEALFGSLLPVPSLDKFAETKEDNRIPGEILCEDECLTLNIGRKAVILKVTSKGDRPIQVGSHYHFIEVNPYLTFDRRKAYGMRLNIAAGTAVRFEPGDCKSVTLVSIEGNKVIRGGNAIADGPVNETNLEAAMHAVRSKGFGHEEEKDASEGFTKEDPNCPFNTFIHRKEYANKYGPTTGDKIRLGDTNLLAEIEKDYALYGDECVFGGGKVIRDGMGQSCGHPPAISLDTVITNAVIIDYTGIIKADIGIKDGLIASIGKAGNPDIMNGVFSNMIIGANTEVIAGEGLIVTAGAIDCHVHYICPQLVYEAISSGITTLVGGGTGPAAGTRATTCTPSPTQMRLMLQSTDDLPLNFGFTGKGSSSKPDELHEIIKAGAMGLKLHEDWGSTPAAIDNCLTIAEHHDIQINIHTDTLNEAGFVEHSIAAFKGRTIHTYHSEGAGGGHAPDIIKVCGIKNVLPSSTNPTRPLTSNTIDEHLDMLMVCHHLDREIPEDLAFAHSRIRKKTIAAEDVLNDIGAISIISSDSQAMGRVGEVISRTWQTADKMKAQTGPLKCDSSDNDNFRIRRYIAKYTINPAIANGFSQYVGSVEVGKLADLVMWKPSFFGTKPEMVIKGGMVAWADIGDPNASIPTPEPVKMRPMYGTLGKAGGALSIAFVSKAALDQRVNVLYGLNKRVEAVSNVRKLTKLDMKLNDALPEITVDPESYTVKADGKLLCVSEATTVPLSRNYFLF 840
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains Urease_gamma-3la4A04 A:1-100                                                                        --------------------------------Urease_beta-3la4A03 A:133-232                                                                       ---------------------------------------Urease_alpha-3la4A02 A:272-392                                                                                           -----Amidohydro_1-3la4A01 A:398-709                                                                                                                                                                                                                                                                                          ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhh..hhhhhh.eeeeeeee..eeeeeeee........hhhhhh........hhhhh..---.......ee....eee.....eeeeeeeee.....eeee...hhhhh...ee.hhhhhh.eee......eeee....eeeeeeee.....ee........ee.hhhhhhhhhhhhhhhh..........eee...........eeehhhhhhhhh.....eee......eee..ee..........................hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeee.....................eeee....eeee.eeeeeee...hhhhhhhhhh.eeeeeee....hhhhhhh....hhhhhhhhhhhh.....eeeeeee.....hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eee............hhhhhhhh..eeeeee........hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh..hhhhhhhh................eeeehhhhh.....eeee..eeeeeee.............eeee.hhhh.hhhhhh.eeeehhhhhhhhhhhhh....eeee.......hhhhh........eee......eee..ee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_1      --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_2         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UREASE_3  PDB: A:402-840 UniProt: 402-840                                                                                                                                                                                                                                                                                                                                                                                                               PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3la4 A   1 MKLSPREVEKLGLHNAGYLAQKRLARGVRLNYTEAVALIASQIMEYARDGEKTVAQLMcLGQHLLGRRQVLPAVPHLLNAVQVEATFPDGTKLVTVHDPISRENGELQEALFGSLLPVPSLDKFAE---DNRIPGEILCEDECLTLNIGRKAVILKVTSKGDRPIQVGSHYHFIEVNPYLTFDRRKAYGMRLNIAAGTAVRFEPGDcKSVTLVSIEGNKVIRGGNAIADGPVNETNLEAAMHAVRSKGFGHEEEKDASEGFTKEDPNCPFNTFIHRKEYANKYGPTTGDKIRLGDTNLLAEIEKDYALYGDECVFGGGKVIRDGMGQSCGHPPAISLDTVITNAVIIDYTGIIKADIGIKDGLIASIGKAGNPDIMNGVFSNMIIGANTEVIAGEGLIVTAGAIDCHVHYICPQLVYEAISSGITTLVGGGTGPAAGTRATTCTPSPTQMRLMLQSTDDLPLNFGFTGKGSSSKPDELHEIIKAGAMGLkLHEDWGSTPAAIDNCLTIAEHHDIQINIHTDTLNEAGFVEHSIAAFKGRTIHTYHSEGAGGGHAPDIIKVCGIKNVLPSSTNPTRPLTSNTIDEHLDMLMVcHHLDREIPEDLAFAHSRIRKKTIAAEDVLNDIGAISIISSDSQAMGRVGEVISRTWQTADKMKAQTGPLKCDSSDNDNFRIRRYIAKYTINPAIANGFSQYVGSVEVGKLADLVMWKPSFFGTKPEMVIKGGMVAWADIGDPNASIPTPEPVKMRPMYGTLGKAGGALSIAFVSKAALDQRVNVLYGLNKRVEAVSNVRKLTKLDMKLNDALPEITVDPESYTVKADGKLLCVSEATTVPLSRNYFLF 840
                                    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       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590 |     600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840
                                                                                     59-CME                                                            126 130                                                                          207-CME                                                                                                                                                                                                                                                                                    490-KCX                                                                                               592-CME

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 3LA4)

(no "CATH Domain" information available for 3LA4)

Asymmetric Unit(hide GO term definitions)

Chain A (UREA_CANEN | P07374)

molecular function
	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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0009039	urease activity	Catalysis of the reaction: urea + H2O = CO2 + 2 NH3.
biological process
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0043419	urea catabolic process	The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.

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
		ACN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CME	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ 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
		Ala A:554 - Pro A:555	[ RasMol ]
		Arg A:575 - Pro A:576	[ RasMol ]
		Glu A:742 - Pro A:743	[ 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
	3la4
		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
	UREA_CANEN \| P07374
		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)
	3.5.1.5
		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
	UREA_CANEN \| P07374
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	UREA_CANEN \| P07374	:	4goa 4gy7 4h9m

(no "Related Entries Specified in the PDB File" available for 3LA4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (4, 4)

Gene Ontology (7, 7)

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