1GYD - JenaLib

Title :   STRUCTURE OF CELLVIBRIO CELLULOSA ALPHA-L-ARABINANASE

Authors :   D. Nurizzo, J. P. Turkenburg, S. J. Charnock, S. M. Roberts, E. J. Dodson V. A. Mckie, E. J. Taylor, H. J. Gilbert, G. J. Davies

Date :   23 Apr 02 (Deposition) - 23 Aug 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym./Biol. Unit : B

Keywords :   Arabinanase, Hydrolase, Propeller, Catalysis, Cellvibrio, Pseudomonas (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Nurizzo, J. P. Turkenburg, S. J. Charnock, S. M. Roberts, E. J. Dodson, V. A. Mckie, E. J. Taylor, H. J. Gilbert, G. J. Davies
Cellovibrio Cellulosa Alpha-L-Arabinanase 43A Has A Novel Five-Blade Beta-Propeller Fold
Nat. Struct. Biol. V. 9 665 2002
PubMed-ID: 12198486 | Reference-DOI: 10.1038/NSB835

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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 B from PDB  Type:PROTEIN  Length:315
 aligned with ARBA_CELJU | P95470 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:315
                                    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       302       312       322       332       342     
           ARBA_CELJU    33 QVDVHDPVMTREGDTWYLFSTGPGITIYSSKDRVNWRYSDRAFGTEPTWAKRVSPSFDGHLWAPDIYQHKGLFYLYYSVSAFGKNTSAIGVTVNKTLNPASPDYRWEDKGIVIESVPQRDLWNAIDPAIIADDHGQVWMSFGSFWGGLKLFKLNDDLTRPAEPQEWHSIAKLERSVLMDDSQAGSAQIEAPFILRKGDYYYLFASWGLCCRKGDSTYHLVVGRSKQVTGPYLDKTGRDMNQGGGSLLIKGNKRWVGLGHNSAYTWDGKDYLVLHAYEAADNYLQKLKILNLHWDGEGWPQVDEKELDSYISQRLK 347
               SCOP domains d1gydb_ B: alpha-L-arabinanase                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1gydB00 B:33-347 Glycosyl hydrolase domain; family 43                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..eeeeee.ee..eeeee....eeeeeee.......hhhhhh.....eeeeeeeeee..eeeeeeee.......eeeeeeee............eeeeeeeee............eeee.....eeeee......eeeee.............eeeee.................eeeeeeeee..eeeeeeee...........eeeeeee..............hhhh..eeee.....eeeeeeeeeeee..eeeeeeeeee......eeeeeee.ee.....ee...hhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gyd B  33 QVDVHDPVMTREGDTWYLFSTGPGITIYSSKDRVNWRYSDRAFATEPTWAKRVSPSFDGHLWAPDIYQHKGLFYLYYSVSAFGKNTSAIGVTVNKTLNPASPDYRWEDKGIVIESVPQRDLWNAIDPAIIADDHGQVWMSFGSFWGGLKLFKLNDDLTRPAEPQEWHSIAKLERSVLMDDSQAGSAQIEAPFILRKGDYYYLFASWGLCCRKGDSTYHLVVGRSKQVTGPYLDKTGRDMNQGGGSLLIKGNKRWVGLGHNSAYTWDGKDYLVLHAYEAADNYLQKLKILNLHWDGEGWPQVDEKELDSYISQRLK 347
                                    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       302       312       322       332       342

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain B (ARBA_CELJU | P95470)

molecular function
	GO:0046558	arabinan endo-1,5-alpha-L-arabinosidase activity	Catalysis of the endohydrolysis of (1->5)-alpha-arabinofuranosidic linkages in (1->5) arabinans.
	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:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0031222	arabinan catabolic process	The chemical reactions and pathways resulting in the breakdown of arabinan, a polysaccharide composed of arabinose residues.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Visualization

Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 1gyd)

	Sites
(no "Sites" information available for 1gyd)

	Cis Peptide Bonds
		Glu B:194 - Pro B:195	[ RasMol ]
		Gly B:261 - Pro B:262	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1gyd
		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
	ARBA_CELJU \| P95470
		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)
	3.2.1.99
		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

Description