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Title :   CRYSTAL STRUCTURES OF THE LIGANDED AND UNLIGANDED NICKEL BINDING PROTEIN NIKA FROM ESCHERICHIA COLI (NICKEL LIGANDED FORM)

Authors :   J. Heddle, D. J. Scott, S. Unzai, S. -Y. Park, J. R. H. Tame

Date :   22 Jul 03 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nickel Binding Protein, Nickel Liganded Form, Crystal Structure, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Heddle, D. J. Scott, S. Unzai, S. -Y. Park, J. R. H. Tame
Crystal Structures Of The Liganded And Unliganded Nickel-Binding Protein Nika From Escherichia Coli
J. Biol. Chem. V. 278 50322 2003
PubMed-ID: 12960164 | Reference-DOI: 10.1074/JBC.M307941200
(for further references see the PDB file header)

Molecule 1 - NICKEL-BINDING PERIPLASMIC PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NIKA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	NIKA, NICKEL BINDING PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	NI	2	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:621 , HOH A:634 , HOH A:644 , HOH A:710 , HOH A:711	BINDING SITE FOR RESIDUE NI A 503
2	AC2	SOFTWARE	HOH B:320 , HOH B:433 , HOH B:441	BINDING SITE FOR RESIDUE NI B 1503

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:23	-	Pro A:24
2	Arg A:137	-	Pro A:138
3	Ala A:258	-	Pro A:259
4	Ala A:400	-	Pro A:401
5	Asp A:403	-	Pro A:404
6	Thr B:1023	-	Pro B:1024
7	Arg B:1137	-	Pro B:1138
8	Ala B:1258	-	Pro B:1259
9	Ala B:1400	-	Pro B:1401
10	Asp B:1403	-	Pro B:1404

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	NIKA_ECOLI	73-95	2	A:51-73 B:1051-1073

(no "Exon" information available for 1UIV)

Asymmetric/Biological 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:497
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:497
                                    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       
          NIKA_ECOLI     26 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV  522
               SCOP domains d1uiva_ A: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeeeee..eeeeee.....hhhhhhh........hhhhh.................eee.......eeeeee............eeeeee..hhhhhhhhhhh....eee......hhhhhhhhhh....eeeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh...........hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uiv A    4 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIRADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV  500
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493

Chain B from PDB  Type:PROTEIN  Length:496
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:496
                                    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      
          NIKA_ECOLI     26 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP  521
               SCOP domains d1uivb_ B: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------SBP_bac_5-1uivB01 B:1045-1419                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------SBP_bac_5-1uivB02 B:1045-1419                                                                                                                                                                                                                                                                                                                                                          -------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhh......ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee..eeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uiv B 1004 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIRADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 1499
                                  1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313      1323      1333      1343      1353      1363      1373      1383      1393      1403      1413      1423      1433      1443      1453      1463      1473      1483      1493

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Nickel-binding periplasmic protein NikA (18)

Escherichia coli [TaxId: 562] (18)

1a	d1uiva_	A:
1b	d1uivb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_5 (33)

Escherichia coli (strain K12) (12)

1a	SBP_bac_5-1uivB01	B:1045-1419
1b	SBP_bac_5-1uivB02	B:1045-1419

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NIKA_ECOLI | P33590)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0050919	negative chemotaxis	The directed movement of a motile cell or organism towards a lower concentration of a chemical.
	GO:0015675	nickel cation transport	The directed movement of nickel (Ni) cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015833	peptide transport	The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
	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/Biological Unit
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	Cis Peptide Bonds
		Ala A:258 - Pro A:259	[ RasMol ]
		Ala A:400 - Pro A:401	[ RasMol ]
		Ala B:1258 - Pro B:1259	[ RasMol ]
		Ala B:1400 - Pro B:1401	[ RasMol ]
		Arg A:137 - Pro A:138	[ RasMol ]
		Arg B:1137 - Pro B:1138	[ RasMol ]
		Asp A:403 - Pro A:404	[ RasMol ]
		Asp B:1403 - Pro B:1404	[ RasMol ]
		Thr A:23 - Pro A:24	[ RasMol ]
		Thr B:1023 - Pro B:1024	[ RasMol ]

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	1uiv
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1uiu	NICKEL UNLIGANDED FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (12, 12)

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