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Title :   LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG AMP

Authors :   M. Zebisch, P. Schaefer, P. Lauble, N. Straeter

Date :   04 Jun 13 (Deposition) - 17 Jul 13 (Release) - 25 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.69

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

Keywords :   Hydrolase, Apyrase, Atpase, Adpase, Cd39, Purinergic Signalling, Domain Rotation, Transition State, Ntpdase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Zebisch, M. Krauss, P. Schaefer, P. Lauble, N. Straeter
Crystallographic Snapshots Along The Reaction Pathway Of Nucleoside Triphosphate Diphosphohydrolases
Structure V. 21 1460 2013
PubMed-ID: 23830739 | Reference-DOI: 10.1016/J.STR.2013.05.016

Molecule 1 - ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 35-393
	Organism Scientific	:	LEGIONELLA PNEUMOPHILA
	Organism Taxid	:	446
	Synonym	:	NTPDASE1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:52 , THR A:53 , ARG A:56 , MET A:187 , GLY A:188 , GLY A:189 , GLN A:231 , GLY A:299 , ASN A:302 , TYR A:346 , MG A:1394 , HOH A:2006 , HOH A:2014 , HOH A:2057 , HOH A:2098 , HOH A:2107 , HOH A:2163	BINDING SITE FOR RESIDUE AMP A1393
2	AC2	SOFTWARE	AMP A:1393 , HOH A:2005 , HOH A:2006 , HOH A:2057 , HOH A:2087 , HOH A:2095	BINDING SITE FOR RESIDUE MG A1394
3	AC3	SOFTWARE	ARG A:122 , GLY A:156 , HOH A:2060 , ASN B:240 , ASP B:253	BINDING SITE FOR RESIDUE CL A1395
4	AC4	SOFTWARE	GLN A:89 , GLN B:89	BINDING SITE FOR RESIDUE CL A1396
5	AC5	SOFTWARE	SER B:52 , THR B:53 , ARG B:56 , GLY B:188 , GLY B:189 , GLN B:231 , GLY B:299 , ASN B:302 , LEU B:303 , TYR B:346 , TYR B:350 , LEU B:353 , MG B:1396 , HOH B:2004 , HOH B:2011 , HOH B:2043 , HOH B:2080 , HOH B:2119 , HOH B:2141	BINDING SITE FOR RESIDUE AMP B1395
6	AC6	SOFTWARE	AMP B:1395 , HOH B:2003 , HOH B:2004 , HOH B:2043 , HOH B:2068 , HOH B:2080	BINDING SITE FOR RESIDUE MG B1396
7	AC7	SOFTWARE	ASN A:240 , ASP A:253	BINDING SITE FOR RESIDUE CL A1397
8	AC8	SOFTWARE	PHE A:140 , GLN A:143 , TRP A:146 , HOH A:2075	BINDING SITE FOR RESIDUE MG A1398

Asymmetric Unit

No.	Residues
1	A:39	-	A:44
2	A:244	-	A:264
3	A:330	-	A:351
4	B:39	-	B:44
5	B:244	-	B:264
6	B:330	-	B:351

Asymmetric Unit

No.	Residues
1	Lys A:82	-	Pro A:83
2	Lys B:82	-	Pro B:83

(no "SAP(SNP)/Variant" information available for 4BRN)

(no "PROSITE Motif" information available for 4BRN)

(no "Exon" information available for 4BRN)

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:356
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:356
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      
         Q5ZUA2_LEGPH    37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHR 392
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh......eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhh...hhhhhhhhhhhhh...eeeeeehhhhhhhh........eehhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh..........eee.hhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brn A  37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHR 392
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

Chain B from PDB  Type:PROTEIN  Length:358
 aligned with Q5ZUA2_LEGPH | Q5ZUA2 from UniProtKB/TrEMBL  Length:393

    Alignment length:358
                                                                                                                                                                                                                                                                                                                                                                                              393 
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386      | 
         Q5ZUA2_LEGPH    37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELEYWFRQQSQWQLAEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRA-   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeee....eeeeeeeeee.....eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhhh.......eeeeeehhhhhh.hhhhhhhhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.......hhh.eeeeee..eeeeeeeeeee..hhhhhhh....hhhhh..............hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeehhhhhhhh........eehhhhhhhhhhhhh...hhhhhhhhh....hhhhhhhhhhhhhhhhh..........eee.hhhhh..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4brn B  37 NPCEKHSCIAVIDAGSTGSRLHIYSYDTDDTNTPIHIEEIWNKKIKPGFASIQPNSVTIDAYLTMLLADAPIHNIPVYFYATAGMRLLPQSQQKKYYDELDYWFRQQSQWQLVEAKTITGNDEALFDWLAVNYKLDTLKSVQNKSVGVMDMGGASVQIVFPMPKNAEISKHNQVELNIYGQNINLYVHSFLGLGQTEMSHQFLNSPSCFANDYPLPDGESGQGNAPSCKEEVTSLMNSVHKVNQQIQPLLALNPVNEWYSIGGISNLASSQLFHFENSELTNQSLLQQGDNQICHQQWDILNGQYPDDEYLYQYCLLSSYYYALMVDGYGINPNQTIHYIPPEQNLDWTIGVVLHRAL 394
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386

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 4BRN)

(no "CATH Domain" information available for 4BRN)

(no "Pfam Domain" information available for 4BRN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5ZUA2_LEGPH | Q5ZUA2)


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: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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Lys A:82 - Pro A:83	[ RasMol ]
		Lys B:82 - Pro B:83	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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3cj1	STRUCTURE OF RATTUS NORVEGICUS NTPDASE2
3cj7	STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH AMP
3cj9	STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM, AMP AND PHOSPHATE
3cja	STRUCTURE OF RATTUS NORVEGICUS NTPDASE2 IN COMPLEX WITH CALCIUM AND AMPPNP
4bqz	RAT NTPDASE2 IN COMPLEX WITH MG GMPPNP
4br0	RAT NTPDASE2 IN COMPLEX WITH CAAMPNP
4br2	RAT NTPDASE2 IN COMPLEX WITH CA UMPPNP
4br4	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br5	RNNTPDASE2 IN COMPLEX WITH ZNAMPPNP
4br7	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM I, OPEN, APO
4br9	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, APO
4bra	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4brc	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, MG AMPNP COMPLEX
4brd	LEGIONELLA PNEUMOPHILA NTPDASE1 Q193E CRYSTAL FORM II, CLOSED, MG AMPPNP COMPLEX
4bre	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMIC ADENOSINE 5' PHOSPHOVANADATE
4brf	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH A DISTORTED ORTHOMOLYBDATE ION AND AMP
4brg	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG GMPPNP
4brh	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG AND THIAMINE PHOSPHOVANADATE
4bri	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II (CLOSED) IN COMPLEX WITH MG UMPPNP
4brk	LEGIONELLA PNEUMOPHILA NTPDASE1 N302Y VARIANT CRYSTAL FORM III (CLOSED) IN COMPLEX WITH MG UMPPNP
4brl	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM III (CLOSED) IN COMPLEX WITH TRANSITION STATE MIMI GUANOSINE 5'- PHOSPHOVANADATE
4brm	SULFUR SAD PHASING OF THE LEGIONELLA PNEUMOPHILA NTPDASE1 - CRYSTAL FORM III (CLOSED) IN COMPLEX WITH SULFATE
4bro	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM IV (PART- OPEN)
4brp	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM V (PART- OPEN)
4brq	LEGIONELLA PNEUMOPHILA NTPDASE1 CRYSTAL FORM II, CLOSED, IN COMPLEX WITH TWO PHOSPHATES BOUND TO ACTIVE SITE MG AND PRODUCT AMP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

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Gene Ontology (3, 3)

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