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(-) Description

Title :  A TETHERED NIACIN-DERIVED PINCER COMPLEX WITH A NICKEL-CARBON BOND IN LACTATE RACEMASE
 
Authors :  B. Desguin, T. Zhang, P. Soumillion, P. Hols, J. Hu, R. P. Hausinger
Date :  27 Jan 16  (Deposition) - 10 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Isomerase, Racemase, Nickel, Cofactor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Desguin, T. Zhang, P. Soumillion, P. Hols, J. Hu, R. P. Hausinger
Metalloproteins. A Tethered Niacin-Derived Pincer Complex With A Nickel-Carbon Bond In Lactate Racemase.
Science V. 349 66 2015
PubMed-ID: 26138974  |  Reference-DOI: 10.1126/SCIENCE.AAB2272

(-) Compounds

Molecule 1 - LACTATE RACEMIZATION OPERON PROTEIN LARA
    Chains: A, B
    Engineered: YES
    Expression System: LACTOCOCCUS LACTIS
    Expression System Taxid: 1590
    Gene: AB662_09960, ADS73_14595, AKJ11_11795, AN634_09100, AOZ08_01600, IV39_GL000121, JM48_0086, NIZO2877_0389, WU67_00115
    Organism Scientific: LACTOBACILLUS PLANTARUM
    Organism Taxid: 1590
    Synonym: TRANSCRIPTIONAL REGULATOR,UNCHARACTERIZED PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 26)

Asymmetric Unit (3, 26)
No.NameCountTypeFull Name
14EY2Ligand/Ion1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC S-ACID
2NI1Ligand/IonNICKEL (II) ION
3SO423Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
14EY1Ligand/Ion1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC S-ACID
2NI-1Ligand/IonNICKEL (II) ION
3SO411Ligand/IonSULFATE ION
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
14EY1Ligand/Ion1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC S-ACID
2NI-1Ligand/IonNICKEL (II) ION
3SO412Ligand/IonSULFATE ION
Biological Unit 3 (2, 25)
No.NameCountTypeFull Name
14EY2Ligand/Ion1-[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]-5-METHANETHIOYL-PYRIDINE-3-CARBOTHIOIC S-ACID
2NI-1Ligand/IonNICKEL (II) ION
3SO423Ligand/IonSULFATE ION

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:71 , ASP A:72 , THR A:74 , ARG A:75 , ALA A:104 , PHE A:107 , HIS A:108 , SER A:180 , GLY A:181 , LYS A:184 , PRO A:188 , GLY A:189 , SO4 A:502binding site for residue 4EY A 501
02AC2SOFTWAREARG A:75 , HIS A:108 , GLN A:295 , LYS A:298 , 4EY A:501binding site for residue SO4 A 502
03AC3SOFTWAREHIS A:108 , ARG A:109binding site for residue SO4 A 503
04AC4SOFTWAREARG A:109binding site for residue SO4 A 504
05AC5SOFTWAREARG A:320binding site for residue SO4 A 505
06AC6SOFTWARELYS A:10 , ARG A:320binding site for residue SO4 A 506
07AC7SOFTWAREARG A:11 , THR A:12binding site for residue SO4 A 507
08AC8SOFTWARESER A:38 , GLU A:39binding site for residue SO4 A 508
09AC9SOFTWAREGLU A:203 , PRO A:349 , ARG A:350binding site for residue SO4 A 509
10AD1SOFTWAREGLY A:407 , GLN A:408 , ALA A:409 , ALA A:410binding site for residue SO4 A 510
11AD2SOFTWAREARG A:98 , ARG B:98binding site for residue SO4 A 511
12AD3SOFTWAREMET A:132 , ASP A:137 , ASP B:137binding site for residue SO4 A 512
13AD4SOFTWAREPRO B:188 , HIS B:200 , 4EY B:502 , SO4 B:503binding site for residue NI B 501
14AD5SOFTWAREARG B:75 , HIS B:108 , HIS B:174 , TYR B:294 , GLN B:295 , LYS B:298 , NI B:501 , 4EY B:502binding site for residue SO4 B 503
15AD6SOFTWAREARG B:109 , GLN B:291 , ASN B:292 , ASP B:321 , HIS B:323binding site for residue SO4 B 504
16AD7SOFTWAREARG B:320binding site for residue SO4 B 505
17AD8SOFTWAREGLY B:121 , GLU B:122binding site for residue SO4 B 506
18AD9SOFTWARESER B:38 , GLU B:39 , LYS B:246binding site for residue SO4 B 507
19AE1SOFTWAREARG B:350binding site for residue SO4 B 508
20AE2SOFTWAREGLU B:203 , PRO B:349 , ARG B:350binding site for residue SO4 B 509
21AE3SOFTWARESER B:207 , PRO B:208binding site for residue SO4 B 510
22AE4SOFTWAREHIS B:217binding site for residue SO4 B 511
23AE5SOFTWAREARG B:211 , VAL B:423 , LYS B:424 , ALA B:425 , SER B:426 , SO4 B:513binding site for residue SO4 B 512
24AE6SOFTWARELYS A:143 , LYS B:424 , TRP B:427 , SO4 B:512binding site for residue SO4 B 513
25AE7SOFTWAREHIS B:371 , ARG B:405binding site for residue SO4 B 514
26AE8SOFTWARESER B:71 , ASP B:72 , THR B:74 , ARG B:75 , ALA B:104 , THR B:105 , PHE B:107 , HIS B:108 , PHE B:170 , HIS B:174 , SER B:180 , GLY B:181 , GLY B:182 , ARG B:183 , SER B:185 , VAL B:186 , LEU B:187 , PRO B:188 , GLY B:189 , HIS B:200 , TYR B:294 , NI B:501 , SO4 B:503binding site for Di-peptide 4EY B 502 and LYS B 184

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HUQ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:187 -Pro A:188
2Tyr A:287 -Pro A:288
3Leu B:187 -Pro B:188
4Tyr B:287 -Pro B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HUQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HUQ)

(-) Exons   (0, 0)

(no "Exon" information available for 5HUQ)

(-) 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:433
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....eeee..hhhhhh....hhhhhhhhhhhh.....hhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhheeee....hhh.eeeeee.....eeeeehhhhh..eeee.....ee...ee.hhhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeeeeeee.....eeeeeee..hhhhhhhhhhhhhhheee...eeeeeee........hhhhhhhhhhhhhh.eeeeeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhheeeeee....hhhhhhh...eee.hhhhhhhhhhhhhh....eee.......eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huq A   1 SVAIDLPYDKRTITAQIDDENYAGKLVSQAATYHNKLSEQETVEKSLDNPIGSDKLEELARGKHNIVIISSDHTRPVPSHIITPILLRRLRSVAPDARIRILVATGFHRPSTHEELVNKYGEDIVNNEEIVMHVSTDDSSMVKIGQLPSGGDCIINKVAAEADLLISEGFIESHFFAGFSGGRKSVLPGIASYKTIMANHSGEFINSPKARTGNLMHNSIHKDMVYAARTAKLAFIINVVLDEDKKIIGSFAGDMEAAHKVGCDFVKELSSVPAIDCDIAISTNGGYPLDQNIYQAVKGMTAAEATNKEGGTIIMVAGARDGHGGEGFYHNLADVDDPKEFLDQAINTPRLKTIPDQWTAQIFARILVHHHVIFVSDLVDPDLITNMHMELAKTLDEAMEKAYAREGQAAKVTVIPDGLGVIVKASWSHPQFE 433
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430   


Chain B from PDB  Type:PROTEIN  Length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....eeee..hhhhhh....hhhhhhhhhhhh.....hhhhhhh...eeeeeee......hhhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhhhhhheeee....hhh.eeeeee.....eeeeehhhhh..eeeeeee..ee...ee.hhhhhh.....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh.eeeeeeeee.....eeeeeee..hhhhhhhhhhhhhhheee...eeeeeee........hhhhhhhhhhhhhh.eeeeeeeeee........hhhhhhhhhh..hhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhheeeeee....hhhhhhh...eee.hhhhhhhhhhhhhh....eee.......eeehhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5huq B   1 SVAIDLPYDKRTITAQIDDENYAGKLVSQAATYHNKLSEQETVEKSLDNPIGSDKLEELARGKHNIVIISSDHTRPVPSHIITPILLRRLRSVAPDARIRILVATGFHRPSTHEELVNKYGEDIVNNEEIVMHVSTDDSSMVKIGQLPSGGDCIINKVAAEADLLISEGFIESHFFAGFSGGRKSVLPGIASYKTIMANHSGEFINSPKARTGNLMHNSIHKDMVYAARTAKLAFIINVVLDEDKKIIGSFAGDMEAAHKVGCDFVKELSSVPAIDCDIAISTNGGYPLDQNIYQAVKGMTAAEATNKEGGTIIMVAGARDGHGGEGFYHNLADVDDPKEFLDQAINTPRLKTIPDQWTAQIFARILVHHHVIFVSDLVDPDLITNMHMELAKTLDEAMEKAYAREGQAAKVTVIPDGLGVIVKASWSHPQF 432
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

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(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5HUQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HUQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HUQ)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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