3ZTV - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF HAEMOPHILUS INFLUENZAE NAD NUCLEOTIDASE (NADN)

Authors :   S. Garavaglia, S. Bruzzone, C. Cassani, L. Canella, G. Allegrone, L. St E. Mannino, E. Millo, A. De Flora, M. Rizzi

Date :   12 Jul 11 (Deposition) - 14 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

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

Keywords :   Hydrolase, Nad Pyrophosphatase, Nmn Nucleotidase, Periplasmic Enzyme, Cd73 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Garavaglia, S. Bruzzone, C. Cassani, L. Canella, G. Allegrone, L. Sturla, E. Mannino, E. Millo, A. De Flora, M. Rizzi
The High-Resolution Crystal Structure Of Periplasmic Haemophilus Influenzae Nad Nucleotidase Reveals A Novel Enzymatic Function Of Human Cd73 Related To Nad Metabolism.
Biochem. J. V. 441 131 2012
PubMed-ID: 21933152 | Reference-DOI: 10.1042/BJ20111263

Molecule 1 - NAD NUCLEOTIDASE
	Atcc	:	51907
	Chains	:	A
	EC Number	:	3.1.3.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PET25B
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 25-603
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	71421
	Other Details	:	FRAGMENT CORRESPONDS TO MATURE PROTEIN
	Strain	:	RD KW20
	Synonym	:	NADN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	GOL	1	Ligand/Ion	GLYCEROL
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ADN	2	Ligand/Ion	ADENOSINE
2	GOL	2	Ligand/Ion	GLYCEROL
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:44 , ASP A:94 , ASN A:126 , HIS A:227 , ASP A:250 , ZN A:1599 , HOH A:2012	BINDING SITE FOR RESIDUE ZN A1598
2	AC2	SOFTWARE	ASP A:44 , HIS A:46 , ASP A:94 , HIS A:252 , ZN A:1598 , HOH A:2012	BINDING SITE FOR RESIDUE ZN A1599
3	AC3	SOFTWARE	ASN A:432 , GLY A:434 , GLY A:435 , PHE A:456 , ASN A:458 , SER A:486 , GLY A:488 , TYR A:540 , ASP A:546 , HOH A:2626 , HOH A:2627	BINDING SITE FOR RESIDUE ADN A1600
4	AC4	SOFTWARE	HIS A:52 , THR A:54 , ILE A:67 , TRP A:289 , ALA A:290 , TYR A:291 , ALA A:293 , HOH A:2041	BINDING SITE FOR RESIDUE GOL A1601

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

Asymmetric Unit

No.	Residues
1	Tyr A:271	-	Pro A:272

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	5_NUCLEOTIDASE_1	PS00785	5'-nucleotidase signature 1.	5NTD_HAEIN	37-49	1	A:37-49
2	5_NUCLEOTIDASE_2	PS00786	5'-nucleotidase signature 2.	5NTD_HAEIN	119-130	1	A:119-130

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	5_NUCLEOTIDASE_1	PS00785	5'-nucleotidase signature 1.	5NTD_HAEIN	37-49	2	A:37-49
2	5_NUCLEOTIDASE_2	PS00786	5'-nucleotidase signature 2.	5NTD_HAEIN	119-130	2	A:119-130

(no "Exon" information available for 3ZTV)

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:565
 aligned with 5NTD_HAEIN | P44569 from UniProtKB/Swiss-Prot  Length:603

    Alignment length:566
                                    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       591      
           5NTD_HAEIN    32 HKAVELSILHINDHHSYLEPHETRINLNGQQTKVDIGGFSAVNAKLNKLRKKYKNPLVLHAGDAITGTLYFTLFGGSADAAVMNAGNFHYFTLGNHEFDAGNEGLLKLLEPLKIPVLSANVIPDKNSILYNKWKPYDIFTVDGEKIAIIGLDTVNKTVNSSSPGKDVKFYDEIATAQIMANALKQQGINKIILLSHAGSEKNIEIAQKVNDIDVIVTGDSHYLYGNDELRSLKLPVIYEYPLEFKNPNGDPVFVMEGWAYSAVVGDLGVKFSPEGIASITRKIPHVLMSSHKLQVKNAEGKWTELTGDERKKALDTLKSMKSISLDDHDAKTDMLISKYKSEKDRLAQEIVGVITGSAMPGGSANRIPNKAGSNPEGSIATRFIAETMYNELKTVDLTIQNAGGVRADILPGNVTFNDAYTFLPFGNTLYTYKMEGSLVKQVLEDAMQFALVDGSTGAFPYGAGIRYEANETPNAEGKRLVSVEVLNKQTQQWEPIDDNKRYLVGTNAYVAGGKDGYKTFGKLFNDPKYEGVDTYLPDAESFIKFMKKHPHFEAYTSSNVKFNAST 597
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.........eeeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeee.......hhhhhh..hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhh.....ee...eee............eeeeee..eeeeeeeee.hhhhhhhh.....eee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh....eeee.....eeehhhhhhh...eeee..eeee.....eeeeee......eeeeeeeee.....eeeeeeeeeeee.....eee.....eee.hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhh..eeeeee......hhhhh...........hhhhhhhhhhhhh......eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhhhhhhh..hhhh.eeee.eeeeee.........eeeeeee..-...eee.....eeeeeeehhhhhhhhhhhhhhhhh.hhhhh.eeeeeehhhhhhhhhhhh.eee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----5_NUCLEOTIDAS---------------------------------------------------------------------5_NUCLEOTIDA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ztv A  32 HKAVELSILHINDHHSYLEPHETRINLNGQQTKVDIGGFSAVNAKLNKLRKKYKNPLVLHAGDAITGTLYFTLFGGSADAAVMNAGNFHYFTLGNHEFDAGNEGLLKLLEPLKIPVLSANVIPDKSSILYNKWKPYDIFTVDGEKIAIIGLDTVNKTVNSSSPGKDVKFYDEIATAQIMANALKQQGINKIILLSHAGSEKNIEIAQKVNDIDVIVTGDSHYLYGNDELRSLKLPVIYEYPLEFKNPNGEPVFVMEGWAYSAVVGDLGVKFSPEGIASITRKIPHVLMSSHKLQVKNSEGKWAELTGDERKKALDTLKSMKSISLDDHDAKTDKLIAKYKSEKDRLAQEIVGVITGSAMPGGSANRIPNKAGSNPEGSIATRFIAETMYNELKTVDLTIQNAGGVRADILPGNVTFNDAYTFLPFGNTLYTYKMEGSLVKQVLEDAMQFALVDGSTGAFPYGAGIRYEANETPNAEGKRLVSVEVLNK-TQQWEPIDDNKRYLVGTNAYVAGGKDGYKTFGKLFNDPKYEGVDTYLPDAESFIKFMKKHPHFEAYTSSNVKFNAST 597
                                    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       591      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 519 |                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   521

Chain A from PDB  Type:PROTEIN  Length:565
 aligned with Q4QNY4_HAEI8 | Q4QNY4 from UniProtKB/TrEMBL  Length:603

    Alignment length:566
                                    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       591      
         Q4QNY4_HAEI8    32 HKAVELSILHINDHHSYLEPHETRINLNGQQTKVDIGGFSAVNAKLNKLRKKYKNPLVLHAGDAITGTLYFTLFGGSADAAVMNAGNFHYFTLGNHEFDAGNEGLLKLLEPLKIPVLSANVIPDKSSILYNKWKPYDIFTVDGEKIAIIGLDTVNKTVNSSSPGKDVKFYDEIATAQIMANALKQQGINKIILLSHAGSEKNIEIAQKVNDIDVIVTGDSHYLYGNDELRSLKLPVIYEYPLEFKNPNGEPVFVMEGWAYSAVVGDLGVKFSPEGIASITRKIPHVLMSSHKLQVKNSEGKWAELTGDERKKALDTLKSMKSISLDDHDAKTDKLIAKYKSEKDRLAQEIVGVITGSAMPGGSANRIPNKAGSNPEGSIATRFIAETMYNELKTVDLTIQNAGGVRADILPGNVTFNDAYTFLPFGNTLYTYKMEGSLVKQVLEDAMQFALVDGSTGAFPYGAGIRYEANETPNAEGKRLVSVEVLNKQTQQWEPIDDNKRYLVGTNAYVAGGKDGYKTFGKLFNDPKYEGVDTYLPDAESFIKFMKKHPHFEAYTSSNVKFNAST 597
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.........eeeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeee.......hhhhhh..hhhhhhhhhhh...eee..hhhhhhhhhhhhhhhh.....ee...eee............eeeeee..eeeeeeeee.hhhhhhhh.....eee.hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh....eeee.....eeehhhhhhh...eeee..eeee.....eeeeee......eeeeeeeee.....eeeeeeeeeeee.....eee.....eee.hhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhh..eeeeee......hhhhh...........hhhhhhhhhhhhh......eeeee.hhh......eeeehhhhhhhh....eeeeeeeehhhhhhhhhhhhhhhhh..hhhh.eeee.eeeeee.........eeeeeee..-...eee.....eeeeeeehhhhhhhhhhhhhhhhh.hhhhh.eeeeeehhhhhhhhhhhh.eee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ztv A  32 HKAVELSILHINDHHSYLEPHETRINLNGQQTKVDIGGFSAVNAKLNKLRKKYKNPLVLHAGDAITGTLYFTLFGGSADAAVMNAGNFHYFTLGNHEFDAGNEGLLKLLEPLKIPVLSANVIPDKSSILYNKWKPYDIFTVDGEKIAIIGLDTVNKTVNSSSPGKDVKFYDEIATAQIMANALKQQGINKIILLSHAGSEKNIEIAQKVNDIDVIVTGDSHYLYGNDELRSLKLPVIYEYPLEFKNPNGEPVFVMEGWAYSAVVGDLGVKFSPEGIASITRKIPHVLMSSHKLQVKNSEGKWAELTGDERKKALDTLKSMKSISLDDHDAKTDKLIAKYKSEKDRLAQEIVGVITGSAMPGGSANRIPNKAGSNPEGSIATRFIAETMYNELKTVDLTIQNAGGVRADILPGNVTFNDAYTFLPFGNTLYTYKMEGSLVKQVLEDAMQFALVDGSTGAFPYGAGIRYEANETPNAEGKRLVSVEVLNK-TQQWEPIDDNKRYLVGTNAYVAGGKDGYKTFGKLFNDPKYEGVDTYLPDAESFIKFMKKHPHFEAYTSSNVKFNAST 597
                                    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       591      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 519 |                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   521

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 3ZTV)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (Q4QNY4_HAEI8 | Q4QNY4)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + 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).

Chain A (5NTD_HAEIN | P44569)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + 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: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
		Tyr A:271 - Pro A:272	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
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	3ztv
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	Q4QNY4_HAEI8 \| Q4QNY4
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	3.1.3.5
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UniProtKB/Swiss-Prot
	5NTD_HAEIN \| P44569	:	3zu0
	Q4QNY4_HAEI8 \| Q4QNY4	:	3zu0

3zu0	STRUCTURE OF HAEMOPHILUS INFLUENZAE NAD NUCLEOTIDASE (NADN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 15)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File