2X8F - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   NATIVE STRUCTURE OF ENDO-1,5-ALPHA-L-ARABINANASES FROM BACILLUS SUBTILIS

Authors :   D. De Sanctis, J. M. Inacio, P. F. Lindley, I. De Sa-Nogueira, I. Bento

Date :   09 Mar 10 (Deposition) - 23 Mar 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

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

Reference :   D. De Sanctis, J. M. Inacio, P. F. Lindley, I. De Sa-Nogueira, I. Bento
New Evidence For The Role Of Calcium In The Glycosidase Reaction Of Gh43 Arabinanases.
Febs J. V. 277 4562 2010
PubMed-ID: 20883454 | Reference-DOI: 10.1111/J.1742-4658.2010.07870.X

Molecule 1 - ENDO-ALPHA-1,5-L-ARABINANASE
	Chains	:	A, B
	EC Number	:	3.2.1.99
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 21)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	GOL	10	Ligand/Ion	GLYCEROL
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	4	Ligand/Ion	SODIUM ION
6	PO4	2	Ligand/Ion	PHOSPHATE ION
7	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	-1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	-1	Ligand/Ion	SODIUM ION
6	PO4	1	Ligand/Ion	PHOSPHATE ION
7	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	-1	Ligand/Ion	SODIUM ION
6	PO4	1	Ligand/Ion	PHOSPHATE ION
7	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:93 , ARG A:125 , MET A:151 , GLU A:152 , HOH A:2278	BINDING SITE FOR RESIDUE PO4 A1471
02	AC2	SOFTWARE	HIS A:318 , HOH A:2009 , HOH A:2012 , HOH A:2104 , HOH A:2105 , HOH A:2144 , HOH A:2194	BINDING SITE FOR RESIDUE CA A1472
03	AC3	SOFTWARE	ASN A:406 , LYS A:407 , ASN A:408	BINDING SITE FOR RESIDUE GOL A1473
04	AC4	SOFTWARE	ASP A:103 , VAL A:104 , THR A:105 , HOH A:2015 , HOH A:2016	BINDING SITE FOR RESIDUE NA A1474
05	AC5	SOFTWARE	VAL A:73 , TYR A:84 , HOH A:2058 , HOH A:2059 , HOH A:2222	BINDING SITE FOR RESIDUE NA A1475
06	AC6	SOFTWARE	ASN A:135 , ILE A:136 , GLU A:137	BINDING SITE FOR RESIDUE GOL A1476
07	AC7	SOFTWARE	PHE A:48 , ASP A:324 , TYR A:367	BINDING SITE FOR RESIDUE GOL A1477
08	AC8	SOFTWARE	THR A:311 , GLY A:312 , TYR A:313 , PHE A:338 , ARG A:348 , ARG A:366 , HOH A:2269 , HOH A:2279	BINDING SITE FOR RESIDUE GOL A1478
09	AC9	SOFTWARE	SER A:123 , PRO A:124 , TYR A:189 , HOH A:2138 , HOH A:2280 , HOH A:2281	BINDING SITE FOR RESIDUE GOL A1479
10	BC1	SOFTWARE	HIS A:37 , HIS A:54 , LEU A:246 , ARG A:337	BINDING SITE FOR RESIDUE MPD A1480
11	BC2	SOFTWARE	HIS B:37 , ASP B:38 , TRP B:100 , VAL B:170 , ASP B:171 , GLU B:224 , LEU B:246 , HIS B:318 , MRD B:1481 , HOH B:2013 , HOH B:2300	BINDING SITE FOR RESIDUE TRS B1471
12	BC3	SOFTWARE	TRP B:93 , ARG B:125 , MET B:151 , GLU B:152 , HOH B:2301	BINDING SITE FOR RESIDUE PO4 B1472
13	BC4	SOFTWARE	HIS B:318 , HOH B:2012 , HOH B:2014 , HOH B:2016 , HOH B:2105 , HOH B:2148 , HOH B:2203	BINDING SITE FOR RESIDUE CA B1473
14	BC5	SOFTWARE	ASP B:103 , VAL B:104 , THR B:105 , HOH B:2018 , HOH B:2036	BINDING SITE FOR RESIDUE NA B1474
15	BC6	SOFTWARE	VAL B:73 , TYR B:84 , HOH B:2060 , HOH B:2061 , HOH B:2241	BINDING SITE FOR RESIDUE NA B1475
16	BC7	SOFTWARE	THR B:311 , GLY B:312 , TYR B:313 , ARG B:348 , ARG B:366 , HOH B:2200 , HOH B:2291 , HOH B:2302	BINDING SITE FOR RESIDUE GOL B1476
17	BC8	SOFTWARE	LYS B:434 , LYS B:435 , ASN B:459 , THR B:460 , SER B:461	BINDING SITE FOR RESIDUE GOL B1477
18	BC9	SOFTWARE	PHE B:353 , MET B:354 , LEU B:372 , HOH B:2209 , HOH B:2280 , HOH B:2303	BINDING SITE FOR RESIDUE GOL B1478
19	CC1	SOFTWARE	ASP B:324 , TYR B:367 , HOH B:2304	BINDING SITE FOR RESIDUE GOL B1479
20	CC2	SOFTWARE	GLU B:43 , THR B:44 , ASN B:45 , GLN B:106 , GLY B:413 , GLU B:414 , MET B:415 , THR B:416 , HOH B:2305 , HOH B:2306	BINDING SITE FOR RESIDUE GOL B1480
21	CC3	SOFTWARE	HIS B:37 , HIS B:54 , ARG B:337 , TRS B:1471	BINDING SITE FOR RESIDUE MRD B1481

(no "SS Bond" information available for 2X8F)

Asymmetric Unit

No.	Residues
1	Gly A:138	-	Pro A:139
2	Gly A:264	-	Pro A:265
3	Gly B:138	-	Pro B:139
4	Gly B:264	-	Pro B:265

(no "SAP(SNP)/Variant" information available for 2X8F)

(no "PROSITE Motif" information available for 2X8F)

(no "Exon" information available for 2X8F)

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:443
 aligned with EABN2_BACSU | P42293 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   469 
                                    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       457       467 | 
          EABN2_BACSU    28 KPIFKEVSVHDPSIIETNGTFYVFGSHLASAKSNDLMQWQQLTTSVSNDNPLIPNVYEELKETFEWAQSDTLWAADVTQLADGKYYMYYNACRGDSPRSAMGVAVADNIEGPYKNKGIFLKSGMEGTSSDGTPYDATKHPNVVDPHTFFDKDGKLWMVYGSYSGGIFILEMNPKTGFPLPGQGYGKKLLGGNHSRIEGPYVLYNPDTQYYYLYLSYGGLDATGGYNIRVARSKKPDGPYYDAEGNPMLDVRGKGGTFFDDRSIEPYGVKLMGSYTFETENEKGTGYVSPGHNSAYYDEKTGRSYLIFHTRFPGRGEEHEVRVHQLFMNKDGWPVAAPYRYAGETLKEVKQKDITGTYKLIQHGKDISADIKQTINIQLNKNHTISGEMTGTWRKTGKNTADITLAGKKYNGVFLRQWDSVREKNVMTFSVLNTSGEAVWGSK-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..eeeee.....eeee......eeee...........hhhhhhhhhhhhhh.......eeee.....eeeeeeee......eeeeeeee.......eeeeeeeee.......................eeee.....eeeee......eeeee...............eeee......eeeeeeeee....eeeeeeee.........eeeeeee..............hhhh........hhhhhh...eeee..ee.........eeeeeeeeeeee......eeeeeeee........eeeeeeeee.....eee.............hhhhhheeeeeee............eeeee....eeee...eeeeee...eeeeee..eeeeeeeeeeee....eeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8f A  28 KPIFKEVSVHDPSIIETNGTFYVFGSHLASAKSNDLMQWQQLTTSVSNDNPLIPNVYEELKETFEWAQSDTLWAADVTQLADGKYYMYYNACRGDSPRSAMGVAVADNIEGPYKNKGIFLKSGMEGTSSDGTPYDATKHPNVVDPHTFFDKDGKLWMVYGSYSGGIFILEMNPKTGFPLPGQGYGKKLLGGNHSRIEGPYVLYNPDTQYYYLYLSYGGLDATGGYNIRVARSKKPDGPYYDAEGNPMLDVRGKGGTFFDDRSIEPYGVKLMGSYTFETENEKGTGYVSPGHNSAYYDEKTGRSYLIFHTRFPGRGEEHEVRVHQLFMNKDGWPVAAPYRYAGETLKEVKQKDITGTYKLIQHGKDISADIKQTINIQLNKNHTISGEMTGTWRKTGKNTADITLAGKKYNGVFLRQWDSVREKNVMTFSVLNTSGEAVWGSKA 470
                                    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       457       467

Chain B from PDB  Type:PROTEIN  Length:443
 aligned with EABN2_BACSU | P42293 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   469 
                                    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       457       467 | 
          EABN2_BACSU    28 KPIFKEVSVHDPSIIETNGTFYVFGSHLASAKSNDLMQWQQLTTSVSNDNPLIPNVYEELKETFEWAQSDTLWAADVTQLADGKYYMYYNACRGDSPRSAMGVAVADNIEGPYKNKGIFLKSGMEGTSSDGTPYDATKHPNVVDPHTFFDKDGKLWMVYGSYSGGIFILEMNPKTGFPLPGQGYGKKLLGGNHSRIEGPYVLYNPDTQYYYLYLSYGGLDATGGYNIRVARSKKPDGPYYDAEGNPMLDVRGKGGTFFDDRSIEPYGVKLMGSYTFETENEKGTGYVSPGHNSAYYDEKTGRSYLIFHTRFPGRGEEHEVRVHQLFMNKDGWPVAAPYRYAGETLKEVKQKDITGTYKLIQHGKDISADIKQTINIQLNKNHTISGEMTGTWRKTGKNTADITLAGKKYNGVFLRQWDSVREKNVMTFSVLNTSGEAVWGSK-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee..eeeee.hhh.eeee......eeee...........hhhhhhhhhhhhhh.......eeee.....eeeeeeee......eeeeeeee.......eeeeeeeee.......................eeee.....eeeee......eeeee...............eeee......eeeeeeeee....eeeeeeee.........eeeeeee..............hhhh........hhhhh....eeee..ee.........eeeeeeeeeeee......eeeeeeee........eeeeeeeee.....eee.............hhhhhheeeeeee............eeeee....eeee...eeeeee...eeeeee..eeeeeeeeeeee....eeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8f B  28 KPIFKEVSVHDPSIIETNGTFYVFGSHLASAKSNDLMQWQQLTTSVSNDNPLIPNVYEELKETFEWAQSDTLWAADVTQLADGKYYMYYNACRGDSPRSAMGVAVADNIEGPYKNKGIFLKSGMEGTSSDGTPYDATKHPNVVDPHTFFDKDGKLWMVYGSYSGGIFILEMNPKTGFPLPGQGYGKKLLGGNHSRIEGPYVLYNPDTQYYYLYLSYGGLDATGGYNIRVARSKKPDGPYYDAEGNPMLDVRGKGGTFFDDRSIEPYGVKLMGSYTFETENEKGTGYVSPGHNSAYYDEKTGRSYLIFHTRFPGRGEEHEVRVHQLFMNKDGWPVAAPYRYAGETLKEVKQKDITGTYKLIQHGKDISADIKQTINIQLNKNHTISGEMTGTWRKTGKNTADITLAGKKYNGVFLRQWDSVREKNVMTFSVLNTSGEAVWGSKA 470
                                    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       457       467

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 2X8F)

(no "CATH Domain" information available for 2X8F)

(no "Pfam Domain" information available for 2X8F)

Asymmetric Unit(hide GO term definitions)

Chain A,B (EABN2_BACSU | P42293)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:138 - Pro A:139	[ RasMol ]
		Gly A:264 - Pro A:265	[ RasMol ]
		Gly B:138 - Pro B:139	[ RasMol ]
		Gly B:264 - Pro B:265	[ RasMol ]

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2x8s	CRYSTAL STRUCTURE OF THE ABN2 D171A MUTANT IN COMPLEX WITH ARABINOTRIOSE
2x8t	CRYSTAL STRUCTURE OF THE ABN2 H318A MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 21)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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