1OI8 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (P90C, L424C)

Authors :   R. Schultz-Heienbrok, T. Maier, N. Straeter

Date :   10 Jun 03 (Deposition) - 10 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Metalloprotein, Hydrolase, Domain Movement, Disulfide Engineering, Udp-Sugar Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Schultz-Heienbrok, T. Maier, N. Straeter
Trapping A 96 Degree Domain Rotation In Two Distinct Conformations By Engineered Disulfide Bridges
Protein Sci. V. 13 1811 2004
PubMed-ID: 15215524 | Reference-DOI: 10.1110/PS.04629604
(for further references see the PDB file header)

Molecule 1 - PROTEIN USHA
	Chains	:	A, B
	EC Number	:	3.1.3.5, 3.6.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	DISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS
	Synonym	:	5-NUCLEOTIDASE

		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 (3, 8)

No.	Name	Count	Type	Full Name
1	CO3	2	Ligand/Ion	CARBONATE ION
2	MN	4	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , MN A:1552 , CO3 A:1554	BINDING SITE FOR RESIDUE MN A1551
2	AC2	SOFTWARE	ASP A:41 , HIS A:43 , ASP A:84 , GLN A:254 , MN A:1551 , CO3 A:1554	BINDING SITE FOR RESIDUE MN A1552
3	AC3	SOFTWARE	ARG A:410 , PRO A:428 , PHE A:429 , HOH A:2381 , HOH A:2474	BINDING SITE FOR RESIDUE SO4 A1553
4	AC4	SOFTWARE	ASP A:41 , ASP A:84 , ASN A:116 , HIS A:117 , HIS A:217 , HIS A:252 , GLN A:254 , MN A:1551 , MN A:1552 , HOH A:2475	BINDING SITE FOR RESIDUE CO3 A1554
5	AC5	SOFTWARE	ASP B:41 , HIS B:43 , ASP B:84 , GLN B:254 , MN B:1552 , CO3 B:1554	BINDING SITE FOR RESIDUE MN B1551
6	AC6	SOFTWARE	ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , MN B:1551 , CO3 B:1554	BINDING SITE FOR RESIDUE MN B1552
7	AC7	SOFTWARE	ARG B:410 , PHE B:429 , HOH B:2438 , HOH B:2439 , HOH B:2440	BINDING SITE FOR RESIDUE SO4 B1553
8	AC8	SOFTWARE	ASP B:41 , HIS B:43 , ASP B:84 , ASN B:116 , HIS B:117 , HIS B:217 , HIS B:252 , GLN B:254 , MN B:1551 , MN B:1552 , HOH B:2203 , HOH B:2441	BINDING SITE FOR RESIDUE CO3 B1554

Asymmetric Unit

No.	Residues
1	A:90	-	A:424
2	A:258	-	A:275
3	B:90	-	B:424
4	B:258	-	B:275

Asymmetric Unit

No.	Residues
1	Ser A:534	-	Pro A:535
2	Ser B:534	-	Pro B:535

(no "SAP(SNP)/Variant" information available for 1OI8)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	5_NUCLEOTIDASE_1	PS00785	5'-nucleotidase signature 1.	USHA_ECOLI	34-46	2	A:34-46 B:34-46
2	5_NUCLEOTIDASE_2	PS00786	5'-nucleotidase signature 2.	USHA_ECOLI	109-120	2	A:109-120 B:109-120

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	5_NUCLEOTIDASE_1	PS00785	5'-nucleotidase signature 1.	USHA_ECOLI	34-46	1	A:34-46 -
2	5_NUCLEOTIDASE_2	PS00786	5'-nucleotidase signature 2.	USHA_ECOLI	109-120	1	A:109-120 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	5_NUCLEOTIDASE_1	PS00785	5'-nucleotidase signature 1.	USHA_ECOLI	34-46	1	- B:34-46
2	5_NUCLEOTIDASE_2	PS00786	5'-nucleotidase signature 2.	USHA_ECOLI	109-120	1	- B:109-120

(no "Exon" information available for 1OI8)

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:526
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      550 
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    | 
           USHA_ECOLI    26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ-   -
               SCOP domains d1oi8a2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1oi8a1 A:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                             - SCOP domains
               CATH domains 1oi8A01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1oi8A02 A:363-549 5'-nucleotidase;  Domain 2                                                                                                                                               -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee...............hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhh.hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee....ee....eeeeee..eeeeeeeee..hhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh....eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhh.........eeee.eeeeee..eeeeeee..ee.....eeeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhhh..hhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi8 A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVCESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVCKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQE 551
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545

Chain B from PDB  Type:PROTEIN  Length:526
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:526
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      550 
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545    | 
           USHA_ECOLI    26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQ-   -
               SCOP domains d1oi8b2 B:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d1oi8b1 B:363-550 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                             - SCOP domains
               CATH domains 1oi8B01 B:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             1oi8B02 B:363-549 5'-nucleotidase;  Domain 2                                                                                                                                               -- CATH domains
           Pfam domains (1) --------Metallophos-1oi8B01 B:34-256                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------5_nucleotid_C-1oi8B03 B:363-511                                                                                                                      ---------------------------------------- Pfam domains (1)
           Pfam domains (2) --------Metallophos-1oi8B02 B:34-256                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------5_nucleotid_C-1oi8B04 B:363-511                                                                                                                      ---------------------------------------- Pfam domains (2)
         Sec.struct. author ......eeeeeeee...............hhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhh.hhhhhhhhhhhh..eee.hhhhhh.hhhhhhhhhhhh...ee...eee....ee....eeeeee..eeeeeeeee..hhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh....eeeeeee...hhhhh......hhhhhhhhh......eee.........eee..ee............eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhhh.eeeee......hhhhhh...hhhhhhhhhhhhhhhh..eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhh.........eeee.eeeeee..eeeeeee..ee.....eeeeeeehhhhhhhhhh........eeeeeeehhhhhhhhhhhhh..hhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi8 B  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVCESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVCKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSWQE 551
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Purple Acid Phosphatase; chain A, domain 2 (87)

Homologous Superfamily: [code=3.60.21.10, no name defined] (83)

Escherichia coli. Organism_taxid: 562. (3)

1a	1oi8A01	A:26-362
1b	1oi8B01	B:26-362

Architecture: Alpha-Beta Complex (3881)

Topology: 5'-nucleotidase; domain 2 (9)

Homologous Superfamily: 5'-nucleotidase; Domain 2 (9)

Escherichia coli. Organism_taxid: 562. (3)

2a	1oi8A02	A:363-549
2b	1oi8B02	B:363-549

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calcineurin (56)

Family: Metallophos (45)

Escherichia coli (strain K12) (4)

1a	Metallophos-1oi8B01	B:34-256
1b	Metallophos-1oi8B02	B:34-256

Clan: no clan defined [family: 5_nucleotid_C] (8)

Family: 5_nucleotid_C (8)

Escherichia coli (strain K12) (4)

2a	5_nucleotid_C-1oi8B03	B:363-511
2b	5_nucleotid_C-1oi8B04	B:363-511

Asymmetric Unit(hide GO term definitions)

Chain A,B (USHA_ECOLI | P07024)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
	GO:0008768	UDP-sugar diphosphatase activity	Catalysis of the reaction: UDP-sugar + H2O = UMP + sugar 1-phosphate.
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0009166	nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
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.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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	1oi8
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	3.1.3.5
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UniProtKB/Swiss-Prot
	USHA_ECOLI \| P07024	:	1ho5 1hp1 1hpu 1oid 1oie 1ush 2ush 4wwl

1ho5	5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE ANDPHOSPHATE
1hp1	5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP
1hpu	5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP
1oid	5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (S228C, P513C)
1oie	5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (S228C, P513C)
1ush	5'-NUCLEOTIDASE FROM E. COLI
2ush	5'-NUCLEOTIDASE FROM E. COLI

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (10, 10)

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