4G9I

Crystal structure of T.kodakarensis HypF

PDB DOI: https://doi.org/10.2210/pdb4G9I/pdb

Classification: TRANSFERASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-07-24 Released: 2012-10-24
Deposition Author(s): Tominaga, T., Watanabe, S., Matsumi, R., Atomi, H., Imanaka, T., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.50 Å
R-Value Free: 0.300
R-Value Work: 0.279
R-Value Observed: 0.279

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the [NiFe]-hydrogenase maturation protein HypF from Thermococcus kodakarensis KOD1.

Tominaga, T., Watanabe, S., Matsumi, R., Atomi, H., Imanaka, T., Miki, K.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1153-1157

PubMed: 23027738 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S1744309112036421
Primary Citation of Related Structures:
4G9I

PubMed Abstract:
HypF is involved in the biosynthesis of the CN ligand of the NiFe(CN)(2)CO centre of [NiFe]-hydrogenases. Here, the full-length structure of HypF from Thermococcus kodakarenesis is reported at 4.5 Å resolution. The N-terminal acylphosphatase-like (ACP) domain interacts with the zinc-finger domain with some flexibility in its relative position. Molecular-surface analysis shows that a deep pocket formed between the ACP and zinc-finger domains is highly conserved and has positive potential. These results suggest that the positively charged pocket identified is involved in the hydrolysis of carbamoyl phosphate and the formation of a carbamoyl intermediate.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 527.03 kDa
Atom Count: 36,065
Modelled Residue Count: 4,573
Deposited Residue Count: 4,632
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrogenase maturation protein HypF	A, B, C, D, E A, B, C, D, E, F	772	Thermococcus kodakarensis KOD1	Mutation(s): 0 Gene Names: hypF, TK1997 EC: 6.2
UniProt
Find proteins for Q5JII4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JII4 Go to UniProtKB: Q5JII4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JII4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth F]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth D], S [auth E], T [auth E], U [auth E], V [auth F], W [auth F], X [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F]