3R4Z - JenaLib

Title :   CRYSTAL STRUCTURE OF ALPHA-NEOAGAROBIOSE HYDROLASE (ALPHA-NABH) IN COMPLEX WITH ALPHA-D-GALACTOPYRANOSE FROM SACCHAROPHAGUS DEGRADANS 2-40

Authors :   S. Lee, J. Y. Lee, S. C. Ha, D. H. Shin, K. H. Kim, W. G. Bang, S. H. Kim, I. G. C

Date :   18 Mar 11 (Deposition) - 01 Feb 12 (Release) - 01 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

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

Keywords :   Agar Metabolism, Neoagarobiose, 3, 6-Anhydro-L-Galactose, Alpha-D- Galactopyranose, Bioenergy, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Ha, S. Lee, J. Lee, H. T. Kim, H. J. Ko, K. H. Kim, I. G. Choi
Crystal Structure Of A Key Enzyme In The Agarolytic Pathway Alpha-Neoagarobiose Hydrolase From Saccharophagus Degradans 2-40
Biochem. Biophys. Res. Commun. V. 412 238 2011
PubMed-ID: 21810409 | Reference-DOI: 10.1016/J.BBRC.2011.07.073

Compounds

Molecule 1 - GLYCOSYL HYDROLASE FAMILY 32, N TERMINAL
	Chains	:	A, B
	EC Number	:	3.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJL
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SDE_2657
	Organism Scientific	:	SACCHAROPHAGUS DEGRADANS
	Organism Taxid	:	203122
	Strain	:	2-40
	Synonym	:	ALPHA-NEOAGAROBIOSE HYDROLASE

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:87 , TRP A:89 , LYS A:222 , GLU A:224 , ARG A:235 , HIS A:264 , HOH A:392 , HOH A:441 , HOH A:447 , HOH A:481 , HOH A:703 , HOH A:714 , SER B:358 , TYR B:359 , GLN B:361	BINDING SITE FOR RESIDUE GLA A 375
2	AC2	SOFTWARE	SER A:358 , TYR A:359 , GLN A:361 , PHE B:87 , TRP B:89 , LYS B:222 , GLU B:224 , ARG B:235 , HIS B:264 , HOH B:404 , HOH B:460 , HOH B:464 , HOH B:590 , HOH B:644 , HOH B:663	BINDING SITE FOR RESIDUE GLA B 375

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:134	-	Gly A:135
2	Ala A:146	-	Pro A:147
3	Gly A:166	-	Pro A:167
4	Gly A:249	-	Pro A:250
5	Asn A:257	-	Pro A:258
6	Ala B:146	-	Pro B:147
7	Gly B:166	-	Pro B:167
8	Gly B:249	-	Pro B:250
9	Asn B:257	-	Pro B:258

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 A from PDB  Type:PROTEIN  Length:358
 aligned with Q21HB2_SACD2 | Q21HB2 from UniProtKB/TrEMBL  Length:368

    Alignment length:362
                                                                                                                                                                                                                                                                                                                                                                                                 368  
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368  
         Q21HB2_SACD2     9 KLSKASLRAIERGYDEKGPEWLFEFDITPLKGDLAYEEGVIRRDPSAVLKVDDEYHVWYTKGEGETVGFGSDNPEDKVFPWDKTEVWHATSKDKITWKEIGPAIQRGAAGAYDDRAVFTPEVLRHNGTYYLVYQTVKAPYLNRSLEHIAIAYSDSPFGPWTKSDAPILSPENDGVWDTDEDNRFLVKEKGSFDSHKVHDPCLMFFNNRFYLYYKGETMGESMNMGGREIKHGVAIADSPLGPYTKSEYNPITNSGHEVAVWPYKGGMATMLTTDGPEKNTCQWAEDGINFDIMSHIKGAPEAVGFFRPESDSDDPISGIEWGLSHKYDASWNWNYLCFFKTRRQVLDAGSYQQTGDSGAV--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eeeeeee.ee.......eeee.....eee..eeeeeeeeee.....................eeeeeee....eeeeeeeee...........eeeeeeeeee..eeeeeeeee..........eeeeeee.......ee............ee.........eee.......eeeeeeeeee..eeeeeeeee.....ee..ee.eeeeeeee.......ee..............eeee..eeeeee........eeeee......eeeee........ee...----...hhhh.eeeeeee......eeeeeeeeee...............eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r4z A   9 KLSKASLRAIERGYDEKGPEWLFEFDITPLKGDLAYEEGVIRRDPSAVLKVDDEYHVWYTKGEGETVGFGSDNPEDKVFPWDKTEVWHATSKDKITWKEIGPAIQRGAAGAYDDRAVFTPEVLRHNGTYYLVYQTVKAPYLNRSLEHIAIAYSDSPFGPWTKSDAPILSPENDGVWDTDEDNRFLVKEKGSFDSHKVHDPCLMFFNNRFYLYYKGETMGESMNMGGREIKHGVAIADSPLGPYTKSEYNPITNSGHEVAVWPYKGGMATMLTTDGPEKNTCQWAEDGINFDIMSHIKGAPEAVGFFRP----DDPISGIEWGLSHKYDASWNWNYLCFFKTRRQVLDAGSYQQTGDSGAVHH 370
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       | -  |    328       338       348       358       368  
                                                                                                                                                                                                                                                                                                                                             316  321

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q21HB2_SACD2 | Q21HB2 from UniProtKB/TrEMBL  Length:368

    Alignment length:363
                                                                                                                                                                                                                                                                                                                                                                                                 368   
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368   
         Q21HB2_SACD2     9 KLSKASLRAIERGYDEKGPEWLFEFDITPLKGDLAYEEGVIRRDPSAVLKVDDEYHVWYTKGEGETVGFGSDNPEDKVFPWDKTEVWHATSKDKITWKEIGPAIQRGAAGAYDDRAVFTPEVLRHNGTYYLVYQTVKAPYLNRSLEHIAIAYSDSPFGPWTKSDAPILSPENDGVWDTDEDNRFLVKEKGSFDSHKVHDPCLMFFNNRFYLYYKGETMGESMNMGGREIKHGVAIADSPLGPYTKSEYNPITNSGHEVAVWPYKGGMATMLTTDGPEKNTCQWAEDGINFDIMSHIKGAPEAVGFFRPESDSDDPISGIEWGLSHKYDASWNWNYLCFFKTRRQVLDAGSYQQTGDSGAV---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.....eeeeeee.ee.......eeee.....eee..eeeeeeeeee.....................eeeeeee....eeeeeeeee...........eeeeeeeeee..eeeeeeeee..........eeeeeee.......ee............ee.........eee.......eeeeeeeeee..eeeeeeeee.....ee..ee.eeeeeeee.......ee..............eeee..eeeeee........eeeee......eeeee........ee...----...hhhh.eeeeeee......eeeeeeeeee...............eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r4z B   9 KLSKASLRAIERGYDEKGPEWLFEFDITPLKGDLAYEEGVIRRDPSAVLKVDDEYHVWYTKGEGETVGFGSDNPEDKVFPWDKTEVWHATSKDKITWKEIGPAIQRGAAGAYDDRAVFTPEVLRHNGTYYLVYQTVKAPYLNRSLEHIAIAYSDSPFGPWTKSDAPILSPENDGVWDTDEDNRFLVKEKGSFDSHKVHDPCLMFFNNRFYLYYKGETMGESMNMGGREIKHGVAIADSPLGPYTKSEYNPITNSGHEVAVWPYKGGMATMLTTDGPEKNTCQWAEDGINFDIMSHIKGAPEAVGFFRP----DDPISGIEWGLSHKYDASWNWNYLCFFKTRRQVLDAGSYQQTGDSGAVHHH 371
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       | -  |    328       338       348       358       368   
                                                                                                                                                                                                                                                                                                                                             316  321

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (3, 3)

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	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:146 - Pro A:147	[ RasMol ]
		Ala B:146 - Pro B:147	[ RasMol ]
		Asn A:134 - Gly A:135	[ RasMol ]
		Asn A:257 - Pro A:258	[ RasMol ]
		Asn B:257 - Pro B:258	[ RasMol ]
		Gly A:166 - Pro A:167	[ RasMol ]
		Gly A:249 - Pro A:250	[ RasMol ]
		Gly B:166 - Pro B:167	[ RasMol ]
		Gly B:249 - Pro B:250	[ RasMol ]

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