2USH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   5'-NUCLEOTIDASE FROM E. COLI

Authors :   T. Knofel, N. Strater

Date :   24 Sep 98 (Deposition) - 15 Jun 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.22

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

Keywords :   5'-Nucleotidase, Udp-Sugar Hydrolase, Phosphatase, Hydrolase (Phosphoric Monoester), Periplasmic Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Knofel, N. Strater
X-Ray Structure Of The Escherichia Coli Periplasmic 5'-Nucleotidase Containing A Dimetal Catalytic Site.
Nat. Struct. Biol. V. 6 448 1999
PubMed-ID: 10331872 | Reference-DOI: 10.1038/8253
(for further references see the PDB file header)

Molecule 1 - 5'-NUCLEOTIDASE
	Chains	:	A, B
	EC Number	:	3.1.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Taxid	:	562
	Gene	:	USHA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	UDP-SUGAR HYDROLASE

		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 (2, 13)

No.	Name	Count	Type	Full Name
1	WO4	4	Ligand/Ion	TUNGSTATE(VI)ION
2	ZN	9	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	WO4	2	Ligand/Ion	TUNGSTATE(VI)ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	WO4	2	Ligand/Ion	TUNGSTATE(VI)ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:41 , HIS A:43 , ASP A:84 , GLN A:254 , ZN A:602 , HOH A:883	BINDING SITE FOR RESIDUE ZN A 601
02	AC2	SOFTWARE	ASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , ZN A:601 , HOH A:883	BINDING SITE FOR RESIDUE ZN A 602
03	AC3	SOFTWARE	ASP B:41 , HIS B:43 , ASP B:84 , GLN B:254 , ZN B:602 , HOH B:880	BINDING SITE FOR RESIDUE ZN B 601
04	AC4	SOFTWARE	ASP B:41 , ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , ZN B:601 , HOH B:880	BINDING SITE FOR RESIDUE ZN B 602
05	AC5	SOFTWARE	WO4 A:702 , LYS B:322 , WO4 B:704	BINDING SITE FOR RESIDUE WO4 B 701
06	AC6	SOFTWARE	ARG A:375 , WO4 A:703 , ARG B:410 , WO4 B:701 , WO4 B:704	BINDING SITE FOR RESIDUE WO4 A 702
07	AC7	SOFTWARE	ARG A:375 , ARG A:379 , ARG A:410 , WO4 A:702 , ZN A:709 , ARG B:375 , WO4 B:704	BINDING SITE FOR RESIDUE WO4 A 703
08	AC8	SOFTWARE	WO4 A:702 , WO4 A:703 , ARG B:410 , WO4 B:701	BINDING SITE FOR RESIDUE WO4 B 704
09	AC9	SOFTWARE	ASP A:194 , HIS B:226 , GLU B:235	BINDING SITE FOR RESIDUE ZN B 705
10	BC1	SOFTWARE	HIS A:226 , GLU A:235 , GLU B:225	BINDING SITE FOR RESIDUE ZN B 706
11	BC2	SOFTWARE	ASP A:374 , ASP A:376 , ASP B:29 , ASP B:376	BINDING SITE FOR RESIDUE ZN A 707
12	BC3	SOFTWARE	HIS A:289 , GLU A:290 , LYS A:293 , GLU B:326	BINDING SITE FOR RESIDUE ZN A 708
13	BC4	SOFTWARE	WO4 A:703	BINDING SITE FOR RESIDUE ZN A 709
14	ZNA	UNKNOWN	ASP A:41 , HIS A:43 , ASP A:84 , ASN A:116 , HIS A:217 , HIS A:252 , GLN A:254	ZN BINDING SITE
15	ZNB	UNKNOWN	ASP B:41 , HIS B:43 , ASP B:84 , ASN B:116 , HIS B:217 , HIS B:252 , GLN B:254	ZN BINDING SITE

Asymmetric Unit

No.	Residues
1	A:258	-	A:275
2	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 2USH)

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 2USH)

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:506
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:524
                                    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 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSW 549
               SCOP domains d2usha2 A:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d2usha1 A:363-549 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                             SCOP domains
               CATH domains 2ushA01 A:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             2ushA02 A:363-546 5'-nucleotidase;  Domain 2                                                                                                                                            --- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee................hhhhhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhh...eee..hhhh...hhhhhhhhhh...eee...eee..........eeeeee..eeeeeeeee.hhh..-----....eee..hhhhhhhhhhhhhh.....eeeeeee....hhh........hhhhhhh.......eee............................eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eee.------..eee........hhhhhhhhhhhhhhhhhh..eeeee.......hhhh.....hhhhhhhhhhhhhh....eeeehhh.......eeeehhhhhhh.....eeeeeeeehhhhhhhhhhhhh........eeee.......-------...........eeeeeeehhhh..hhh.........eeeeeeehhhhhhhhhhhh....hhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ush A  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAK-----YFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKV------SERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAK-------KIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSW 549
                                    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       | -    |  335       345       355       365       375       385       395       405       415       425       435       445       455       465     |   -   |   485       495       505       515       525       535       545    
                                                                                                                                                                                 177   183                                                                                                                                         323    330                                                                                                                                          471     479

Chain B from PDB  Type:PROTEIN  Length:520
 aligned with USHA_ECOLI | P07024 from UniProtKB/Swiss-Prot  Length:550

    Alignment length:524
                                    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 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFVAKDGKLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSW 549
               SCOP domains d2ushb2 B:26-362 5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain                                                                                                                                                                                                                                                                   d2ushb1 B:363-549 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain                                                                                                             SCOP domains
               CATH domains 2ushB01 B:26-362  [code=3.60.21.10, no name defined]                                                                                                                                                                                                                                                                                             2ushB02 B:363-548 5'-nucleotidase;  Domain 2                                                                                                                                              - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhh...hhhhhhhhhh...eee..hhhh...hhhhhhhhhh...eee...eee..........eeeeee..eeeeeeeee.........hhh...eee..hhhhhhhhhhhhhh.....eeeeeee....hhh........hhhhhhh.......eee............................eee..eeee.......eeeeeeeeee..eeeeeeeeeee...eeeee.....eeeee........hhhhhhhhhhhhhhhhhh..eeeee.......hhhh.....hhhhhhhhhhhhhh....eeeehhh.......eeeehhhhhhh.....eeeeeeeehhhhhhhhhhhhh........eeee.....----................eeeeeeehhhh..hhh.........eeeeeeehhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------5_NUCLEOTIDAS--------------------------------------------------------------5_NUCLEOTIDA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ush B  26 YEQDKTYKITVLHTNDHHGHFWRNEYGEYGLAAQKTLVDGIRKEVAAEGGSVLLLSGGDINTGVPESDLQDAEPDFRGMNLVGYDAMAIGNHEFDNPLTVLRQQEKWAKFPLLSANIYQKSTGERLFKPWALFKRQDLKIAVIGLTTDDTAKIGNPEYFTDIEFRKPADEAKLVIQELQQTEKPDIIIAATHMGHYDNGEHGSNAPGDVEMARALPAGSLAMIVGGHSQDPVCMAAENKKQVDYVPGTPCKPDQQNGIWIVQAHEWGKYVGRADFEFRNGEMKMVNYQLIPVNLKKKVTWEDGKSERVLYTPEIAENQQMISLLSPFQNKGKAQLEVKIGETNGRLEGDRDKVRFVQTNMGRLILAAQMDRTGADFAVMSGGGIRDSIEAGDISYKNVLKVQPFGNVVVYADMTGKEVIDYLTAVAQMKPDSGAYPQFANVSFV----KLNDLKIKGEPVDPAKTYRMATLNFNATGGDGYPRLDNKPGYVNTGFIDAEVLKAYIQKSSPLDVSVYEPKGEVSW 549
                                    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    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     469  474

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 "Pfam Domain" information available for 2USH)

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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	Cis Peptide Bonds
		Ser A:534 - Pro A:535	[ RasMol ]
		Ser B:534 - Pro B:535	[ RasMol ]

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	2ush
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	USHA_ECOLI \| P07024	:	1ho5 1hp1 1hpu 1oi8 1oid 1oie 1ush 4wwl

(no "Related Entries Specified in the PDB File" available for 2USH)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (15, 15)

SS Bonds (2, 2)

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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