3I5O - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE X-RAY CRYSTAL STRUCTURE OF A THERMOPHILIC CELLOBIOSE BINDING PROTEIN BOUND WITH CELLOPENTAOSE

Authors :   M. J. Cuneo, H. W. Hellinga

Date :   06 Jul 09 (Deposition) - 21 Jul 09 (Release) - 22 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Cellulose, Carbohydrate-Binding Protein, Periplasmic Binding Protein, Cellopentaose, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Cuneo, L. S. Beese, H. W. Hellinga
Structural Analysis Of Semi-Specific Oligosaccharide Recognition By A Cellulose-Binding Protein Of Thermotoga Maritima Reveals Adaptations For Functional Diversification Of The Oligopeptide Periplasmic Binding Protein Fold.
J. Biol. Chem. V. 284 33217 2009
PubMed-ID: 19801540 | Reference-DOI: 10.1074/JBC.M109.041624

Molecule 1 - OLIGOPEPTIDE ABC TRANSPORTER, PERIPLASMIC OLIGOPEPTIDE- BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM0031, TM_0031
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Synonym	:	CELLOBIOSE-BINDING PROTEIN

		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 (1, 10)

No.	Name	Count	Type	Full Name
1	BGC	10	Ligand/Ion	BETA-D-GLUCOSE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	BGC	5	Ligand/Ion	BETA-D-GLUCOSE

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	BGC	5	Ligand/Ion	BETA-D-GLUCOSE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:101 , PRO A:102 , GLY A:103 , GLY A:104 , TRP A:457 , ALA A:458 , BGC A:2242 , HOH A:2379 , HOH A:2390 , HOH A:2404 , HOH A:2530	BINDING SITE FOR RESIDUE BGC A 2241
02	AC2	SOFTWARE	TRP A:427 , ALA A:538 , BGC A:2241 , BGC A:2243 , HOH A:2344 , HOH A:2396 , HOH A:2401 , HOH A:2428 , HOH A:2436 , HOH A:2458 , HOH A:2652	BINDING SITE FOR RESIDUE BGC A 2242
03	AC3	SOFTWARE	ASP A:262 , TRP A:427 , TRP A:536 , BGC A:2242 , BGC A:2244 , HOH A:2248 , HOH A:2299 , HOH A:2344 , HOH A:2398	BINDING SITE FOR RESIDUE BGC A 2243
04	AC4	SOFTWARE	GLY A:13 , ALA A:14 , TRP A:511 , TRP A:536 , BGC A:2243 , BGC A:2245 , HOH A:2295 , HOH A:2346 , HOH A:2520 , HOH A:2575	BINDING SITE FOR RESIDUE BGC A 2244
05	AC5	SOFTWARE	GLY A:13 , TRP A:16 , ASN A:216 , GLY A:232 , LEU A:233 , PHE A:234 , TRP A:381 , ASP A:383 , TRP A:384 , TRP A:511 , BGC A:2244 , HOH A:2319	BINDING SITE FOR RESIDUE BGC A 2245
06	AC6	SOFTWARE	GLY B:101 , PRO B:102 , GLY B:103 , GLY B:104 , TRP B:457 , ALA B:458 , BGC B:2247 , HOH B:2267 , HOH B:2310 , HOH B:2495 , HOH B:2530	BINDING SITE FOR RESIDUE BGC B 2246
07	AC7	SOFTWARE	TRP B:427 , ALA B:538 , BGC B:2246 , BGC B:2248 , HOH B:2257 , HOH B:2323 , HOH B:2396 , HOH B:2399 , HOH B:2484 , HOH B:2492	BINDING SITE FOR RESIDUE BGC B 2247
08	AC8	SOFTWARE	ASP B:262 , TRP B:427 , TRP B:536 , BGC B:2247 , BGC B:2249 , HOH B:2257 , HOH B:2313 , HOH B:2600	BINDING SITE FOR RESIDUE BGC B 2248
09	AC9	SOFTWARE	GLY B:13 , ALA B:14 , TRP B:511 , TRP B:536 , BGC B:2248 , BGC B:2250 , HOH B:2320 , HOH B:2339 , HOH B:2520	BINDING SITE FOR RESIDUE BGC B 2249
10	BC1	SOFTWARE	GLY B:13 , TRP B:16 , ASN B:216 , GLY B:232 , LEU B:233 , PHE B:234 , TRP B:381 , ASP B:383 , TRP B:384 , TRP B:511 , BGC B:2249 , HOH B:2258	BINDING SITE FOR RESIDUE BGC B 2250

(no "SS Bond" information available for 3I5O)

Asymmetric Unit

No.	Residues
1	Glu A:256	-	Pro A:257
2	Gly A:371	-	Pro A:372
3	His A:435	-	Pro A:436
4	Glu B:256	-	Pro B:257
5	Gly B:371	-	Pro B:372
6	His B:435	-	Pro B:436

(no "SAP(SNP)/Variant" information available for 3I5O)

(no "PROSITE Motif" information available for 3I5O)

(no "Exon" information available for 3I5O)

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:582
 aligned with Q9WXN8_THEMA | Q9WXN8 from UniProtKB/TrEMBL  Length:606

    Alignment length:582
                                    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       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603  
         Q9WXN8_THEMA    24 SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVVEFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWELWEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGVRVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLDPEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT 605
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeee...................hhhhhh....eeee....eeee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhhh.....hhhhheeeeeeee..eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............eeeeeee..eeeeee................eeeee...hhhhhhhhhhhh...ee.......hhhhhh....eee.........eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..ee.....ee.........eeee....hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeeee...eee...ee.....................hhhhhhee....................eehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3i5o A   2 SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVVEFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWELWEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGVRVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLDPEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT 583
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581

Chain B from PDB  Type:PROTEIN  Length:582
 aligned with Q9WXN8_THEMA | Q9WXN8 from UniProtKB/TrEMBL  Length:606

    Alignment length:582
                                    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       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603  
         Q9WXN8_THEMA    24 SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVVEFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWELWEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGVRVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLDPEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT 605
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhh.eeeee...................hhhhhh....eeee....eeee..eeeeeeee..eeeeee............hhhhhhhhhhhhhhhh.....hhhhheeeeeeee..eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.............eeeeeee..eeeeee................eeeee...hhhhhhhhhhhh...ee.......hhhhhh....eee.........eeeeeeeee........hhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..ee.....ee.........eeee....hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh..eeeeeee...eee...ee.....................hhhhhhee............hhhhh...eehhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3i5o B   2 SLPREDTVYIGGALWGPATTWNLYAPQSTWGTDQFMYLPAFQYDLGRDAWIPVIAERYEFVDDKTLRIYIRPEARWSDGVPITADDFVYALELTKELGIGPGGGWDTYIEYVKAVDTKVVEFKAKEENLNYFQFLSYSLGAQPMPKHVYERIRAQMNIKDWINDKPEEQVVSGPYKLYYYDPNIVVYQRVDDWWGKDIFGLPRPKYLAHVIYKDNPSASLAFERGDIDWNGLFIPSVWELWEKKGLPVGTWYKKEPYFIPDGVGFVYVNNTKPGLSDPAVRKAIAYAIPYNEMLKKAYFGYGSQAHPSMVIDLFEPYKQYIDYELAKKTFGTEDGRIPFDLDMANKILDEAGYKKGPDGVRVGPDGTKLGPYTISVPYGWTDWMMMCEMIAKNLRSIGIDVKTEFPDFSVWADRMTKGTFDLIISWSVGPSFDHPFNIYRFVLDKRLSKPVGEVTWAGDWERYDNDEVVELLDKAVSTLDPEVRKQAYFRIQQIIYRDMPSIPAFYTAHWYEYSTKYWINWPSEDNPAWFRPSPWHADAWPTLFIISKKSDPQPVPSWLGTVDEGGIEIPTAKIFEDLQKAT 583
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581

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 3I5O)

(no "CATH Domain" information available for 3I5O)

(no "Pfam Domain" information available for 3I5O)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9WXN8_THEMA | Q9WXN8)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
biological process
	GO:0042884	microcin transport	The directed movement of microcin, a class of glycine-rich, bactericidal peptides (antibiotics) produced by some enteric bacteria, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:256 - Pro A:257	[ RasMol ]
		Glu B:256 - Pro B:257	[ RasMol ]
		Gly A:371 - Pro A:372	[ RasMol ]
		Gly B:371 - Pro B:372	[ RasMol ]
		His A:435 - Pro A:436	[ RasMol ]
		His B:435 - Pro B:436	[ RasMol ]

Biological Units
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	Q9WXN8_THEMA \| Q9WXN8	:	2o7i 4jsd 4jso

2o7i	THE X-RAY CRYSTAL STRUCTURE OF A THERMOPHILIC CELLOBIOSE BINDING PROTEIN BOUND WITH CELLOBIOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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