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(-) Description

Title :  CRYSTAL STRUCTURE OF NMRA, A NEGATIVE TRANSCRIPTIONAL REGULATOR (MONOCLINIC FORM)
 
Authors :  D. K. Stammers, J. Ren, K. Leslie, C. E. Nichols, H. K. Lamb, S. Cocklin, A A. R. Hawkins
Date :  16 Oct 01  (Deposition) - 20 Feb 02  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold Transcriptional Regulation Short Chain Dehydrogenase Reductase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. K. Stammers, J. Ren, K. Leslie, C. E. Nichols, H. K. Lamb, S. Cocklin, A. Dodds, A. R. Hawkins
The Structure Of The Negative Transcriptional Regulator Nmr Reveals A Structural Superfamily Which Includes The Short-Chain Dehydrogenase/Reductases.
Embo J. V. 20 6619 2001
PubMed-ID: 11726498  |  Reference-DOI: 10.1093/EMBOJ/20.23.6619
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NMRA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRC99A
    Expression System Strain: BL23 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NMRA
    Organism Scientific: EMERICELLA NIDULANS
    Organism Taxid: 162425

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:242 , HOH B:900BINDING SITE FOR RESIDUE CL B 750
2AC2SOFTWAREGLN B:166 , LYS B:251BINDING SITE FOR RESIDUE CL B 751
3AC3SOFTWAREVAL A:252 , ASN A:253BINDING SITE FOR RESIDUE CL A 752
4AC4SOFTWAREASN A:12 , ALA A:13 , THR A:14 , VAL A:36 , HIS A:37BINDING SITE FOR RESIDUE CL A 753
5AC5SOFTWAREASN B:12 , ALA B:13 , THR B:14 , VAL B:36 , HIS B:37BINDING SITE FOR RESIDUE CL B 754
6AC6SOFTWAREARG A:239 , GLN B:106BINDING SITE FOR RESIDUE CL A 755
7AC7SOFTWAREALA B:230 , ARG B:234 , HOH B:1500BINDING SITE FOR RESIDUE CL B 756

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K6J)

(-) Exons   (0, 0)

(no "Exon" information available for 1K6J)

(-) 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:322
 aligned with NMRA_EMENI | Q5AU62 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:349
                                    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         
           NMRA_EMENI     4 QKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFSRPAAGSPKGLGPANGKGAGAGMMQGPGGVISQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
               SCOP domains d1k6ja_ A: Negative transcriptional regulator NmrA                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1k6jA01 A:4-151,A:191-219,A:275-328 NAD(P)-binding Rossmann-like Domain                                                                             1k6jA02 A:152-190,A:220-274,A:329-351  1k6jA01                      1k6jA02 A:152-190,A:220-274,A:329-351                  1k6jA01                                               1k6jA02                - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee.....hhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh...eeeeee..hhhhh........hhhhhhhhhhhhhhh..eeeeee.ee.hhh.........eee.....eeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh..................---------------------------...hhhhhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k6j A   4 QKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFSRPAA---------------------------QRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
                                    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   |     -         -         - |     323       333       343         
                                                                                                                                                                                                                                                                                                                     287                         315                                     


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with NMRA_EMENI | Q5AU62 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:351
                                    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 
           NMRA_EMENI     2 AQQKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFSRPAAGSPKGLGPANGKGAGAGMMQGPGGVISQRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
               SCOP domains d1k6jb_ B: Negative transcriptional regulator NmrA                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -1k6jB01 B:3-151,B:191-219,B:275-328 NAD(P)-binding Rossmann-like Domain                                                                              1k6jB02 B:152-190,B:220-274,B:329-351  1k6jB01                      1k6jB02 B:152-190,B:220-274,B:329-351                  1k6jB01                                               1k6jB02                - CATH domains
           Pfam domains (1) ------NmrA-1k6jB01 B:8-244                                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ------NmrA-1k6jB02 B:8-244                                                                                                                                                                                                                         ------------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ......eee....hhhhhhhhhhhhhh...eeeee....hhhhhhhhh...eeeee.....hhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhh...eeeeee..hhhhh........hhhhhhhhhhhhhh...eeeeee.ee.hhh.........eee.....eeeee.......eeeehhhhhhhhhhhhhhhhhhhhhh..eeee..eeehhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhh...............------------------------------...hhhhhhhh....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k6j B   2 AQQKKTIAVVNATGRQAASLIRVAAAVGHHVRAQVHSLKGLIAEELQAIPNVTLFQGPLLNNVPLMDTLFEGAHLAFINTTSQAGDEIAIGKDLADAAKRAGTIQHYIYSSMPDHSLYGPWPAVPMWAPKFTVENYVRQLGLPSTFVYAGIYNNNFTSLPYPLFQMELMPDGTFEWHAPFDPDIPLPWLDAEHDVGPALLQIFKDGPQKWNGHRIALTFETLSPVQVCAAFSRALNRRVTYVQVPKVEIKVNIPVGYREQLEAIEVVFGEHKAPYFPLPEFSR------------------------------QRVTDEARKLWSGWRDMEEYAREVFPIEEEANGLDWML 352
                                    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  |      -         -         -   |   321       331       341       351 
                                                                                                                                                                                                                                                                                                                    284                            315
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NMRA_EMENI | Q5AU62)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070401    NADP+ binding    Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070405    ammonium ion binding    Interacting selectively and non-covalently with ammonium ions (NH4+).
    GO:0070406    glutamine binding    Interacting selectively and non-covalently with glutamine, 2,5-diamino-5-oxopentanoic acid.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0090295    nitrogen catabolite repression of transcription    A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription of specific genes involved in the metabolism of other nitrogen sources.
    GO:0001081    nitrogen catabolite repression of transcription from RNA polymerase II promoter    A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NMRA_EMENI | Q5AU62: 1k6i 1k6x 1ti7 1xgk 2vus 2vut 2vuu

(-) Related Entries Specified in the PDB File

1k6i CRYSTAL STRUCTURE OF NMRA, A NEGATIVE TRANSCRIPTIONAL REGULATOR (TRIGONAL FORM)