1VK6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NADH PYROPHOSPHATASE (1790429) FROM ESCHERICHIA COLI K12 AT 2.20 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   30 Apr 04 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   1790429, Nadh Pyrophosphatase, Structural Genomics, Jcsg, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Nadh Pyrophosphatase (1790429) From Escherichia Coli K12 At 2. 20 A Resolution
To Be Published
PubMed: search

Molecule 1 - NADH PYROPHOSPHATASE
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NUDC, B3996
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 22)

No.	Name	Count	Type	Full Name
1	MPD	6	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 11)

No.	Name	Count	Type	Full Name
1	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:98 , CYS A:101 , CYS A:116 , CYS A:119	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	ARG A:84 , TRP A:112 , PRO A:125 , GLN A:198 , HOH A:377	BINDING SITE FOR RESIDUE MPD A 302
3	AC3	SOFTWARE	ASP A:2 , LEU A:56 , GLN A:58 , HOH A:317 , HOH A:367	BINDING SITE FOR RESIDUE MPD A 303
4	AC4	SOFTWARE	CYS A:130 , GLY A:159 , TRP A:194 , HOH A:388	BINDING SITE FOR RESIDUE MPD A 304

(no "SS Bond" information available for 1VK6)

Asymmetric Unit

No.	Residues
1	Phe A:196	-	Pro A:197

(no "SAP(SNP)/Variant" information available for 1VK6)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDC_ECOLI	125-248	1	A:125-248
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDC_ECOLI	159-180	1	A:159-180

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDC_ECOLI	125-248	2	A:125-248
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDC_ECOLI	159-180	2	A:159-180

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NUDIX	PS51462	Nudix hydrolase domain profile.	NUDC_ECOLI	125-248	1	A:125-248
2	NUDIX_BOX	PS00893	Nudix box signature.	NUDC_ECOLI	159-180	1	A:159-180

(no "Exon" information available for 1VK6)

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:257
 aligned with NUDC_ECOLI | P32664 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:257
                             1                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       
           NUDC_ECOLI     - -MDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDMGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEMYPSKTEWAMLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVMEESGIKVKNLRYVTSQPWPFPQSLMTAFMAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAMCRAEY 256
               SCOP domains d1vk6a3 A:0-96 NADH pyrophosphatase                                                              d1vk6a4 A:97-125             d1vk6a2 A:126-256 NADH pyrophosphatase                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------NUDIX-like-1vk6A02 A:10-91                                                        -zf-NADH-PPase-1vk6A03 A:93-124  --NUDIX-1vk6A01 A:127-249                                                                                                    ------- Pfam domains
         Sec.struct. author ...ee.....eeeeeeee..eee.hhhh..eee.hhhh....eeeeeee....eeeeee......ee..hhhhhhhhhhhhhhhhhhhhhhhhhh..........eee......eee.....ee....eeeeeeeeee..eeeeeee..........eeee.....hhhhhhhhhhhhhhh.eeeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeee...........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------NUDIX  PDB: A:125-248 UniProt: 125-248                                                                                      -------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------NUDIX_BOX             ---------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vk6 A   0 HmDRIIEKLDHGWWVVSHEQKLWLPKGELPYGEAANFDLVGQRALQIGEWQGEPVWLVQQQRRHDmGSVRQVIDLDVGLFQLAGRGVQLAEFYRSHKYCGYCGHEmYPSKTEWAmLCSHCRERYYPQIAPCIIVAIRRDDSILLAQHTRHRNGVHTVLAGFVEVGETLEQAVAREVmEESGIKVKNLRYVTSQPWPFPQSLmTAFmAEYDSGDIVIDPKELLEANWYRYDDLPLLPPPGTVARRLIEDTVAmCRAEY 256
                             |       9        19        29        39        49        59     |  69        79        89        99     | 109    |  119       129       139       149       159       169      |179       189       199 |   | 209       219       229       239       249 |     
                             |                                                              65-MSE                                 105-MSE  114-MSE                                                       176-MSE                  201-MSE                                           251-MSE 
                             1-MSE                                                                                                                                                                                                     205-MSE

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Nudix (141)

Superfamily: Nudix (141)

Family: NADH pyrophosphatase (2)

Protein domain: NADH pyrophosphatase (2)

Escherichia coli [TaxId: 562] (2)

1a	d1vk6a2	A:126-256
1b	d1vk6a3	A:0-96

Class: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: NADH pyrophosphatase intervening domain (2)

Family: NADH pyrophosphatase intervening domain (2)

Protein domain: NADH pyrophosphatase intervening domain (2)

Escherichia coli [TaxId: 562] (2)

d1vk6a4

A:97-125

(no "CATH Domain" information available for 1VK6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Escherichia coli (strain K12) (28)

NUDIX-1vk6A01

A:127-249

Family: NUDIX-like (1)

Escherichia coli (strain K12) (1)

NUDIX-like-1vk6A02

A:10-91

Clan: Zn_Beta_Ribbon (109)

Family: zf-NADH-PPase (1)

Escherichia coli (strain K12) (1)

zf-NADH-PPase-1vk6A03

A:93-124

Asymmetric Unit(hide GO term definitions)

Chain A (NUDC_ECOLI | P32664)


GO:0000210	NAD+ diphosphatase activity	Catalysis of the reaction: NAD+ + H2O = AMP + NMN.
GO:0035529	NADH pyrophosphatase activity	Catalysis of the reaction: NADH + H2O = AMP + NMNH + 2 H+.
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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.

Asymmetric Unit
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		Phe A:196 - Pro A:197	[ RasMol ]

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Description

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