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(-) Description

Title :  X-RAY STRUCTURE OF NIKA IN COMPLEX WITH NI-(L-HIS)2
 
Authors :  H. Lebrette, M. Iannello, J. C. Fontecilla-Camps, C. Cavazza
Date :  03 Dec 12  (Deposition) - 30 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Lebrette, M. Iannello, J. C. Fontecilla-Camps, C. Cavazza
The Binding Mode Of Ni-((L)-His)(2) In Nika Revealed By X-Ray Crystallography.
J. Inorg. Biochem. V. 121C 16 2012
PubMed-ID: 23314594  |  Reference-DOI: 10.1016/J.JINORGBIO.2012.12.010

(-) Compounds

Molecule 1 - NICKEL-BINDING PERIPLASMIC PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NIKA, B3476, JW3441
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 36)

Asymmetric Unit (6, 36)
No.NameCountTypeFull Name
1ACT16Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GOL8Ligand/IonGLYCEROL
4HIS6Mod. Amino AcidHISTIDINE
5NI3Ligand/IonNICKEL (II) ION
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4HIS2Mod. Amino AcidHISTIDINE
5NI-1Ligand/IonNICKEL (II) ION
6SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4HIS2Mod. Amino AcidHISTIDINE
5NI-1Ligand/IonNICKEL (II) ION
6SO41Ligand/IonSULFATE ION
Biological Unit 3 (4, 8)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4HIS2Mod. Amino AcidHISTIDINE
5NI-1Ligand/IonNICKEL (II) ION
6SO41Ligand/IonSULFATE ION

(-) Sites  (36, 36)

Asymmetric Unit (36, 36)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:22 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , HIS A:602 , NI A:603 , HOH A:717BINDING SITE FOR RESIDUE HIS A 601
02AC2SOFTWARETHR A:23 , ARG A:97 , ARG A:137 , TYR A:382 , ARG A:386 , HIS A:416 , HIS A:601 , NI A:603 , ACT A:604BINDING SITE FOR RESIDUE HIS A 602
03AC3SOFTWAREHIS A:416 , HIS A:601 , HIS A:602BINDING SITE FOR RESIDUE NI A 603
04AC4SOFTWARETHR A:23 , GLU A:378 , HIS A:602 , HOH A:714BINDING SITE FOR RESIDUE ACT A 604
05AC5SOFTWAREGLN A:385 , HIS A:395 , HIS A:416 , HOH A:841 , HOH A:843 , HOH A:844BINDING SITE FOR RESIDUE ACT A 605
06AC6SOFTWARETYR A:127 , ARG A:447 , HOH A:827BINDING SITE FOR RESIDUE ACT A 606
07AC7SOFTWARETHR A:203 , ASP A:227BINDING SITE FOR RESIDUE ACT A 607
08AC8SOFTWAREPRO A:159 , LEU A:167BINDING SITE FOR RESIDUE ACT A 608
09AC9SOFTWAREARG A:68BINDING SITE FOR RESIDUE ACT A 609
10BC1SOFTWAREASN A:149 , LYS A:157BINDING SITE FOR RESIDUE ACT A 610
11BC2SOFTWARETRP A:10 , PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223BINDING SITE FOR RESIDUE GOL A 611
12BC3SOFTWAREGLN A:361 , SER A:372 , LEU A:373BINDING SITE FOR RESIDUE GOL A 612
13BC4SOFTWARELYS A:276 , GLU A:320 , THR A:325 , LEU A:326 , ARG A:333 , LYS B:276BINDING SITE FOR RESIDUE GOL A 613
14BC5SOFTWARETYR B:22 , TRP B:100 , ARG B:137 , TRP B:398 , TYR B:402 , HIS B:416 , HIS B:602 , NI B:603 , HOH B:706 , HOH B:806BINDING SITE FOR RESIDUE HIS B 601
15BC6SOFTWARETYR B:22 , THR B:23 , ARG B:97 , ARG B:137 , TYR B:382 , ARG B:386 , HIS B:416 , HIS B:601 , NI B:603 , HOH B:825BINDING SITE FOR RESIDUE HIS B 602
16BC7SOFTWAREHIS B:416 , HIS B:601 , HIS B:602BINDING SITE FOR RESIDUE NI B 603
17BC8SOFTWARELEU B:293 , HIS B:459 , HOH B:728BINDING SITE FOR RESIDUE CL B 604
18BC9SOFTWARESER B:57 , GLU B:58BINDING SITE FOR RESIDUE ACT B 605
19CC1SOFTWARETRP B:54BINDING SITE FOR RESIDUE ACT B 606
20CC2SOFTWARETHR B:441 , HIS B:442BINDING SITE FOR RESIDUE ACT B 607
21CC3SOFTWAREASN B:149 , LYS B:157BINDING SITE FOR RESIDUE ACT B 608
22CC4SOFTWAREGLU B:434BINDING SITE FOR RESIDUE ACT B 609
23CC5SOFTWAREASN B:220 , ALA B:489 , THR B:490 , HOH B:766 , HOH B:796BINDING SITE FOR RESIDUE GOL B 610
24CC6SOFTWAREARG B:68BINDING SITE FOR RESIDUE GOL B 611
25CC7SOFTWAREPHE A:229 , SER A:233 , LEU A:242 , ASN B:302 , LEU B:303 , GLY B:304BINDING SITE FOR RESIDUE GOL B 612
26CC8SOFTWARETYR B:382 , GLN B:385 , PHE B:394 , HIS B:395 , ARG B:396 , HIS B:416 , HOH B:755BINDING SITE FOR RESIDUE SO4 B 613
27CC9SOFTWAREARG B:341 , LYS C:433BINDING SITE FOR RESIDUE ACT B 614
28DC1SOFTWARETYR C:22 , MET C:27 , TRP C:100 , ARG C:137 , TRP C:398 , TYR C:402 , HIS C:416 , HIS C:602 , NI C:603 , HOH C:709BINDING SITE FOR RESIDUE HIS C 601
29DC2SOFTWARETHR C:23 , ARG C:97 , ARG C:137 , TYR C:382 , ARG C:386 , HIS C:416 , HIS C:601 , NI C:603 , HOH C:711 , HOH C:756BINDING SITE FOR RESIDUE HIS C 602
30DC3SOFTWAREHIS C:416 , HIS C:601 , HIS C:602BINDING SITE FOR RESIDUE NI C 603
31DC4SOFTWARELYS C:275 , LYS C:276BINDING SITE FOR RESIDUE ACT C 604
32DC5SOFTWAREARG A:95 , HIS C:442BINDING SITE FOR RESIDUE ACT C 605
33DC6SOFTWARETYR C:382 , GLN C:385 , PHE C:394 , HIS C:395 , ARG C:396 , HIS C:416 , HOH C:755BINDING SITE FOR RESIDUE ACT C 606
34DC7SOFTWAREGLN C:361 , ASP C:370 , VAL C:371 , SER C:372 , LEU C:373BINDING SITE FOR RESIDUE GOL C 607
35DC8SOFTWAREASN B:261 , ASN C:261 , HOH C:738BINDING SITE FOR RESIDUE GOL C 608
36DC9SOFTWARELYS B:433 , ARG C:341BINDING SITE FOR RESIDUE SO4 C 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I8C)

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Thr A:23 -Pro A:24
2Arg A:137 -Pro A:138
3Ala A:258 -Pro A:259
4Ala A:400 -Pro A:401
5Asp A:403 -Pro A:404
6Thr B:23 -Pro B:24
7Arg B:137 -Pro B:138
8Ala B:258 -Pro B:259
9Ala B:400 -Pro B:401
10Asp B:403 -Pro B:404
11Thr C:23 -Pro C:24
12Arg C:137 -Pro C:138
13Ala C:258 -Pro C:259
14Ala C:400 -Pro C:401
15Asp C:403 -Pro C:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I8C)

(-) Exons   (0, 0)

(no "Exon" information available for 4I8C)

(-) Sequences/Alignments

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:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4i8ca_ 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.hhhhhheeeeee....eeeeee.....hhhhhhhh.......hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee..eeee.hhhh...........hhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8c A   2 APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVHH 602
                                    11        21        31        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       601 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            500| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             601 


Chain B from PDB  Type:PROTEIN  Length:501
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4i8cb_ B: 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.hhhhhheeeeee....eeeeee.....hhhhhhh........hhhhh.................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeee....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhhhh...........................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee.eeeee.hhhh...........hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i8c B   3 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPVKHH 602
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       601 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            501| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             601 


Chain C from PDB  Type:PROTEIN  Length:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4i8cc_ C: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhh.eeeeee....eeeeee.....hhhhhhh........hhh.ee..eeeeee........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeee....hhhhhhhhhhh...eeeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh...........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i8c C   4 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPHH 602
                                    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     || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         499| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          601
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I8C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I8C)

(-) Gene Ontology  (12, 12)

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  Cis Peptide Bonds
    Ala A:258 - Pro A:259   [ RasMol ]  
    Ala A:400 - Pro A:401   [ RasMol ]  
    Ala B:258 - Pro B:259   [ RasMol ]  
    Ala B:400 - Pro B:401   [ RasMol ]  
    Ala C:258 - Pro C:259   [ RasMol ]  
    Ala C:400 - Pro C:401   [ RasMol ]  
    Arg A:137 - Pro A:138   [ RasMol ]  
    Arg B:137 - Pro B:138   [ RasMol ]  
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    Thr A:23 - Pro A:24   [ RasMol ]  
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    Thr C:23 - Pro C:24   [ RasMol ]  
 
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  4i8c
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  NIKA_ECOLI | P33590
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        NIKA_ECOLI | P33590: 1uiu 1uiv 1zlq 2noo 3dp8 3e3k 3mvw 3mvx 3mvy 3mvz 3mw0 3mz9 3mzb 3qim 4dcx 4dcy 4i9d 5l8d 5mwu

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